A/N Happy Tuesday! We finally get to see the first proper interaction between Riles and John this chapter, there are definitely a lot of feelings and pain for them to work through, and neither of them are exactly good at expressing themselves.

Enjoy!

Recap -

Elizabeth squeezed her hands together then smiled. "General O'Neill and Mr Woolsey have just left on a Jumper back to Earth. I wanted to tell you all before it's announced officially, but..." she let her words linger in the air. "The expedition will be returning to Atlantis."

—-

Alice sat across from Elizabeth in the smaller briefing room. "We were working with the Genii for a little over three months. They knew we'd abandoned the city and reached out to us. They wanted to... utilise our skills." She said considering her words carefully.

"What did-" Before Elizabeth could finish speaking the door to the briefing room opened and John strolled in.

"Sorry I'm late. I didn't get the memo." He said pointedly.

That's cause you weren't invited, Alice wanted to say. But she held her tongue.

John loudly dragged out a chair and sat down casually next to Elizabeth. Alice attempted to keep the scowl off her face, but judging by Elizabeth's expression she wasn't doing a good job.

Elizabeth glanced uncomfortable between the two of them, sensing the obvious tension hanging in the air. "Alice was just debriefing me about the Genii."

John crossed a leg over the other and leaned back slightly. "Well don't let me interrupt." A slight smirk playing on his lips. "You must have a unique insight."

Alice couldn't look at him, he was purposely trying to irritate her. Pulling her shoulders down, she directed her gaze at Elizabeth. "Like I was just saying, the Genii approached us. Since the expedition left they're the most organised group of humans, willing to go on the offensive against the Wraith." She took in a breath, aware of John's scrutinising gaze. "At first we said no, but they were persistent."

"And that's all it takes." John sneered.

Alice gritted her teeth. "In exchange for our help." she spoke using a carefully controlled tone. "They offered the Athosians food and medical supplies which we desperately needed. And they also agreed to continue helping our other allies like the Taranans."

"And what help, exactly, did you have to give in return?" John said, over annunciating help.

Alice finally turned her gaze to John. "Intel, and support on their ops." She seethed. If he was trying to insinuate she'd slept her way around the Genii ranks he was going to regret it.

He raised an eyebrow. "That's all...What about their weapons programme?"

Alice felt her whole body start to tense. She was starting to loose her cool. "I didn't give them blueprints to build a nuclear bomb if that's what you're asking."

Elizabeth's eyebrows drew together as she considered the two of them. "Alice, please."

She turned back to face Elizabeth, attempting to relax her body slightly. "Mostly... we ran support and recon. Since you left" she put some strain on the word. "The Wraith have been busy setting up new outposts along the boarders of populated solar systems. We were trying to find out what they were up to."

"Did you?" Elizabeth asked.

Alice opened her mouth to answer when John interrupted. "Mostly...? what else did you do?"

She pressed her lips together. "We helped Ladon organise strike teams, and advised on his military strategy." She didn't know why but she felt the sudden urge to defend her actions. "We couldn't let the Wraith establish these new bases. So whenever we could, we would go in and destroy them before they finished constructing them. It wasn't like before...we..." She paused, her voice catching in her throat.

"What is it?" Elizabeth pressed gently.

Taking in a breath she steadied her trembling hands. "Running ops was riskier with the Genii, without the database or MALPs we were heading in blind. Our intel could only tell us so much." She hesitated, thinking about the faces she'd led on their first strike mission. And how many of them didn't come back. "Sometimes...things didn't go to plan."

Elizabeth nodded. "I see. Do you know what were they doing at these outposts?"

Alice shook her head. "We don't know. The Genii weren't too worried about that, they just wanted them gone. No matter the cost."

"Now that sounds more like the Ladon we know." John scowled.

"Y'know he's just trying to protect his people and the rest of this galaxy." Alice snapped back.

John straightened in his chair. "You're defending him now?" His voice was slightly raised and his eyes bored accusingly at her.

Alice felt her blood starting to boil. "Are you questioning my judgement?!"

John didn't answer, his expression told her everything she needed to know though.

"John. Alice." Elizabeth said sharply.

Alice glared at John a moment longer, before tearing away to look at Elizabeth. "Look, my report will include all the details and addresses of the outposts we took out or knew about." She stood up abruptly, unwilling to sit under John's scrutiny.

Elizabeth and John followed suit. "Thank you Alice." Elizabeth said politely.

Turning her back on John she started walking to the door alongside their leader. "With your permission Elizabeth, i'd like to reach out to Ladon and let him know we're back. We've been out of the game, he can help us reestablish ourselves. It's also been a while, and he's probably wondering what's happened to us."

Elizabeth started to nod, but John's voice stopped her. "No."

Alice steeled herself, but she didn't turn around. "I wasn't asking you."

"The Genii have put this expedition at risk more times than we can count. I won't allow you to broadcast our vulnerability to them." He argued back, starting to raise his voice.

Alice whipped her head around to face him, her eyes blazing. "Ladon is a good man, we can trust him. He's-"

"I said no."

"Then you're making a mistake." Alice spat back at him.

"Two years ago this guy almost let you bleed to death right over there." He threw his hand out to point towards the control room.

She raised her voice to match his. "And if it wasn't for him I would be rotting on some Wraith planet."

"That's enough." Elizabeth shouted over the top of them. "Both of you." She took in a breath and lowered her voice. "I will consider your request Alice. But i will not have two of my senior officers getting into a screaming match." Although softer, her voice was full of authority, she narrowed her eyes at the two of them daring them to challenge her.

Alice continued to glare at John. "Yes ma'am. If that's all then." She turned and stormed out of the room.

She couldn't believe his arrogance. Huffing she stomped down the hallway towards the south pier. In the two days since Elizabeth had announced the expedition would be returning she'd barely had time to sleep. People started arriving through the gate in groups - curtesy to one of the Ancient's new ZPMs O'Neill had taken back with him - one after the other just a few hours of O'Neill's return.

The first through the gate were all SG team members. It had made the IOA and the President nervous that the gateway to Earth from Pegasus was currently just being held by one team (and the Daedalus). Alice couldn't complain though, among the first to step through were Evan and Lloyd. Though Evan hadn't been happy with John after he'd found out he hadn't been included on the rescue mission back here.

In all the chaos of moving all the equipment, getting people settled, and trying to regain control of the city's systems, Alice and John hadn't had a chance to talk. Before last night, they'd briefly seen each other in the hallways but avoided eye contact. It was safe to say they had some issues they needed to resolve, but after last night and just now Alice wasn't even sure how to approach him.

She arrived on the isolated balcony, closing her eyes, letting the cool ocean air pass by her. She was still seething, she couldn't believe what he'd said to her, the way he'd said it to her.

Flashback to the previous night

Alice pushed through the crowded mess hall, they'd spent the whole day welcoming back teams and re-installing equipment. Alice's muscles ached and all she wanted was to head back to her quarters and fall into bed. But Elizabeth had organised a celebratory gathering for all the returning personnel, now that all but a few of the expedition personnel had returned.

Typical of all the parties they'd thrown in the city, it had started as a rather classy affair but once everyone had a few drinks in them - especially the military personnel - everything descended into a full blown rave. Someone had dimmed the lights and somehow jerry-rigged their iPod into the mess hall's speaker system, so loud music blasted through the room.

She finally saw who she was looking for, standing amongst a group of soldiers was Evan and Lloyd. "There you are!" she shouted over the loud music.

A beaming smile spread across Evan's face. "Ahhhh Aly-cat!" he yelled, pulling her into a back crunching hug.

"Geez Ev, you're crushing me!" She laughed, trying to push herself off her friend.

"Aw give him a break Als, he's been moping about you for months." Lloyd wrapped his arm around the two of them, a drink in his hand. "I'm never going to see her again, why didn't i stay with her." Lloyd grinned as he did his best impression of a pouting Evan.

Evan flushed and slapped Lloyd's arm off him. "Shut up." he grumbled.

Alice just giggled, it was nice to have her friends back. Lloyd held his hand up in surrender. "Alright, alright. Seriously though it's good to see yah." he ruffled the top of Alice's head. "Is it true you're not banging the Colonel anymore? 'Cause if you're not?" He waggled his eyebrows at her, looking her up and down.

Alice groaned, Lloyd just didn't have any tact. She knew it would come up sooner or later, but she'd been hoping for later.

Evan elbowed their friend in the side. "Come on, enough."

"Touchy, touchy." Lloyd took a big gulp of his drink and looked over towards the make-shift bar. "Alright, drinks are on me. We are celebrating our glorious return."

Alice couldn't help but laugh as he went careening through the crowd to fetch them more drinks. "Sorry about that." Evan leaned down to whisper in Alice's ear, so she would be able to hear him over the music.

"Don't worry about it." She smiled, hoping he would drop the issue.

"Is it true? You and Sheppard aren't getting back together?" His eyes gazed into hers.

She sighed, honestly she didn't really know. They hadn't had a chance to talk about what would happen now they were back. Pressing her lips to his ear so no one else would see, she said. "I don't really want to think about it right now." She pulled back to look in his eyes, pleading for him to drop it.

He nodded, bringing his hand up to push her hair back behind her ear. "Alright. Then let's focus on something else."

Just then Lloyd reappeared with a tray of shots in his hands. "The party is here." Laughing they all grabbed a glass and clinked them together. Alice tipped her head back and tried not to wince as the burning liquid slid down her throat. "And another!" Lloyd placed another glass in each of their hands, with all of them obediently tipping their heads back to drain yet another glass.

Alice wasn't sure how many she ended up having, but with everything going on she couldn't help but want to celebrate having her friends back with her and forget about her troubles with John. And that's when she got into trouble.

Huddled in their small corner, Alice laughed and drank with her friends. To her surprise, the crowd hadn't thinned out too much even though it had to be well past midnight at this point. She'd seen Teyla socialising with some of the scientists from botany, whilst Ronon was arm wrestling with some of the new marines. It would be a miracle if no one broke a wrist.

A small area in the middle of the hall had been cleared to make space for a dance floor. As she glanced around, the smile dropped from her lips and her face instantly flushed in anger.

Across the room she could see John casually resting up against a pillar drinking from a glass, and a woman standing close to him. They were laughing as John leant down to say something in the woman's ear, his signature smirk playing on his face. The woman was beaming up at him with her hand reaching out to stoke his arm. Alice hadn't seen her before, she must've have been a new recruit - but seeing John flirting with her sent a burning sensation through her chest.

She always knew that he'd move on eventually, but she never thought she'd be around to see it.

Alcohol and jealousy were never good bedfellows. She tried to ignore it, to focus on her friends in front of her. But every 30 seconds she'd check over her shoulder to see if they were still there, smiling, talking, touching.

"You okay Aly? It looks like smoke is about to start coming out of your ears…" Evan's tone was soft, caring.

It made her think back to the days she'd spent seeking comfort in his arms. They'd long moved past their feelings for each other, but for a split second Alice considered it. The image already formed in her mind, how much it would take to convince him to fall back into bed with her.

But the image was gone as soon as it had come. She didn't want him, and he didn't want her. Not like that.

"I'm fine." She replied curtly, once again glancing over her shoulder at John and the woman. She grabbed the drink in his hand and finished it for him, before taking his hand and pulling him towards the dance floor. She wanted to wipe the image of John out of her brain. "Let's dance."

Still confused, Evan allowed her to pull him onto the floor. Lloyd and the other boys whooped and cat-called loudly behind them, causing most people in the room to turn and stare at them. Alice didn't let herself worry about them though, she wrapped her arms around Evan's neck and started swaying to the music. Joining the other couples on the dance floor. Despite the amount of alcohol he'd drunk, Evan didn't miss a beat. Placing his hands on her waist. "This hasn't got something to do with the Colonel, does it?"

Alice smiled sweetly, tilting her head to the side. "I don't know what you're talking about."

Even with her senses dulled by the alcohol, she could feel John's eyes boring into her, but she didn't care. She wanted to forget him. Forget the pain. And if her enjoying the moment caused a spark of jealousy in John, then she wasn't going to deny that it made the moment even sweeter.

Evan twisted her around and spun her out, catching her outstretched hand. Laughing Alice looked over to the gathering crowd of marines and airmen. "Come on!" She yelled. That seemed to be all the encouragement Lloyd and the others to join them, jumping up and down around them. Evan released his grip on her waist as they parted and allowed everyone to join in around them. The dance floor became a tight knit group of arms and legs flailing about. She even noticed Ronon joining in at one point, a drink sloshing in his hand. Throwing her head back, Alice grinned and closed her eyes enjoying the moment.

When Alice dared to glance over to where John had been standing, all she saw was an empty gap. She tried looking through the crowds but she couldn't see him or the woman he'd been with anywhere.

Briefly, she wondered if he'd taken her back to his room.

That was the last conscious thought she had the rest of the night. After more drinks were poured, the night became a blur.

Alice woke up to knocking on her door. Groggy and bleary eyed, she slipped out of her bed and headed for the door.

The knocking became more insistent. "Yeah, yeah." she mumbled, yawning waving her hand over the door panel. Standing outside her door was Lloyd and Rodney. Squinting she looked them over, Rodney had his arm up telling her he'd been the one knocking. "What…"

Lloyd was grinning. "Wow Aly, you look…"

Alice held up her finger in Lloyd's face. She was still wearing her uniform from the night before, and she was sure her hair looked like a bird's nest. "Don't even think it Lloyd."

She saw his lips pull into a smile. Rodney cleared his throat impatiently. "Yes, well. Alice, Elizabeth asked me to come by and ask you to debrief her on the Genii situation, and I also need you to come by the lab to help with the instal."

Alice covered her mouth with the back of her hand trying to stifle a yawn. "Sure thing, I'll be by as soon as I can." She turned to Lloyd. "And did you come by just to mock me?" she raised an eyebrow.

His smile turned into a cheeky grin, as he folded his arms across his chest. "Nope, I came by to get our Major."

Alice dropped her hand, confused, "Major…?" Lloyd pointed back into her room.

Knitting her brows together she followed Lloyd's finger. That's when she noticed an extra set of combat boots on the floor and a SG team jacket thrown over her chair. Tilting her eyes up she finally saw Evan asleep on the sofa by the window.

"Um…" she was lost for words, looking between Lloyd's amused face and Rodney's suspicious one. She squinted trying to force herself to remember what had happened last night, from Lloyd's expression she could tell he was trying to suggest something had happened between the two of them. "He was to drunk to make it to his room." she said. Memories of trying to half drag and half carry Evan down the halls came into her mind.

"Sure thing Riley." Lloyd strode past her and into the room. "Come on Major - the Colonel has been looking for you. I can't wait to see his face when sees you."

Alice felt her heart drop through the floor. "You didn't…" Panic flared in her chest as she saw the mischievous look on Lloyd's face. "What did you say to him!" She spun around and stormed after him. "I swear to god Lloyd."

Lloyd let out a bark of laughter, ignoring her and hitting Evan on the shoulder trying to wake him up. "Nothing for you to worry about Riley… Besides I thought you two weren't a thing anymore?"

Evan yawned below them. "Lloyd? Aly?"

Alice grabbed the front of Lloyd's jacket. "Whatever we are is none of your business. Now tell me." She growled.

Lloyd held his hands up in surrender. "I didn't tell him anything. He showed up at my door this morning telling me to collect the Major and that i'd find him in your room."

Alice's throat tightened. She didn't know if she ought to be outraged at his insinuation or embarrassed. Lloyd pulled his jacket out of her grip, "We really need to get going." He grabbed the back of Evan's shirt and hauled him the rest of the way up to his feet.

She stepped back, allowing them to move past her. The smell of stale alcohol hit her and made bile rise in her throat.

Rodney lingered in the doorway as Alice ushered Evan and Lloyd out of the door. "I swear to god Lloyd. Don't think I still couldn't beat your ass." She yelled after him as he led a barely awake Evan down the hall, cackling with laughter. "Shit." She turned to face Rodney. "What!" she said, probably a bit too fiercely.

Rodney paled and took a step backward. "Nothing, I'll…um…I'll see you later."

The door slid shut leaving Alice back in her dark room. Her knees dropped out from underneath her as she slid to the floor groaning. Today was going to be the worst day. She needed to talk to John, hopefully before he heard anything. Though memories of last night coursed through her mind, John with the female scientist. Suddenly, she wondered if the reason he'd left was to be with her. Alice couldn't remember seeing her again after John left. "When did things get so complicated." she folded her hands over her head, dreading the impending conversation that she would have to endure.

Even though she knew she should get up and find John, she found it difficult to move. Not because of the headache that was forming behind her eyes, but because of the fear knotting her stomach together. A significant amount of time had passed, she was sure she still had feelings for him, that much was clear. But what if he didn't feel the same? What if that was it for them…

She agonised over these thoughts for a few minutes, before finally motivating herself to stand up. She pulled on her jacket, taking a moment to fix her appearance then headed out the door steeling herself to deal with John.

It didn't take her long to find him, every morning he was holding briefings with the military teams, updating them on the mission and if they were returning crew then what had changed. She arrived just as BDU clad soldiers started filing out of the briefing room. John spotted her almost immediately, but he turned away and pretended to busy himself with the blueprints and reports on the desk. "If you're looking for Major Lorne he left already." John's voice was cold, Alice winced stepping forward.

"Actually I was looking for you." She rubbed her arm, looking around the room. "I thought we needed to talk."

"I don't think we've got anything to talk about."Alice felt the temperature of the air drop. He still had his back to her. A few moments of silence passed as Alice tried to figure out what to say, her mind suddenly blank. "What do you want to say, Doctor." Her skin prickled, he was purposefully trying to get under her skin.

"I never thought I was going to see you again."

John's head snapped around. "So you just turn to the first man you met? Is that what you're trying to tell me?" His tone was scathing.

"Evan and I are just friends, you know that better than anyone."

He turned back to his documents. "And Ladon. What's he then?"

"Ladon? What the hell has he got to do with this?" Alice yelled.

"You know what. It doesn't matter." John turned around to face her. "You made it very clear that we're done. So I suggest you spend more time focusing on your job."

Alice's mouth felt dry, she took a step towards John. "Fine.

"Colonel, I was-" Alice jumped backwards as a strangers voice interrupted their screaming match.

She had no idea why he had brought up Ladon. And no idea what to say back. Glancing at the entrance a junior office stood in the doorway holding a data pad against her chest. Her face flushed as she realised what she'd just walked in on. "I'm sorry sir." she apologised and started to turn around.

Alice straightened up, narrowing her eyes at John. "Don't worry Lieutenant. I was just leaving." Without another glance at him she stormed out the door, blood pounding in her ears.

Alice felt like her head was about to explode. She let out a few short breaths trying to calm herself down, out of the corner of her eye she caught the time on her watch. "Oh great." She muttered realising she was late to meet with Elizabeth.

End of flashback

Another gust of wind blew across her face, Alice closed her eyes and inhaled, hoping the air would help clear her brought her hands up to rub her face. "There you are." Ronon's voice startled her. "Teyla's been looking for you. Something about the power in the residential block."

Sniffling she wiped her eyes and pushed away from the railing. "Sure. I'll head down there now."

Before she could walk back into the hallway, Ronon grabbed her shoulder. "You okay?" She didn't even know he knew about her little hideaway here, the only other person she'd hung out here with was John. Ronon must've sensed her hesitance. "I heard about what happened."

Alice sighed. "Already... geez. We're back five minutes and I'm already centre of the gossip mill." Taking a step back she rubbed her fingers against her temple. "John just... he." She didn't even know how to put it into words. "He basically accused me of sleeping with Ladon. I have no idea where he got that idea." She rambled, stopping when she noticed Ronon wincing. "What." She glared at him accusingly.

"That might have been my fault..." he said softly. "Sheppard was asking about the Genii and I mentioned you and Ladon were quite close. And that he seemed to have a bit of an affection for you."

Alice groaned, grabbing a fist full of her hair and tugging it. "Why do men have to be so petty. I mean is that what he really thinks of me?!" She growled, letting go of her hair she paced back and forth on the balcony. Her brain filled with so many thoughts she was sure they were about to explode out of her brain. The logical part of her brain told her that she had no right to be angry given what she'd said to him when they'd broken up, that he didn't owe her a conversation. But she was more emotional than that, she wanted to storm back into his office, throw a chair at his head and make him understand. Or maybe at least shoot him with an intar.

But she stopped pacing, taking in a deep breath. Allowing her face to drop to the ground. "God, I don't know how it got to this."

"It may not be my place, but…" Ronon drew in a breath and Alice glanced up to meet his eyes. "He never said it outright, but you meant everything to him. Losing that..." he cleared his throat uncomfortably. "Losing that is almost impossible to deal with."

From his tone and expression, she could tell he wasn't just sympathising. He'd never really spoken about Sateda, and whether he'd left anyone behind. But now she was sure. "I...I never wanted to hurt him." She said pathetically, knowing it was the worst excuse in the book.

"Give him time." Ronon said softly, then turned to leave her alone.

Over the next week she avoided John like the plague, not that they had any reason to see each other. They hadn't restarted off-world missions, and instead were focused on re-establishing themselves in the City and with their close allies - including the Genii. Alice had been there to greet Ladon as he stepped through the gate, and whilst she'd tried to remove herself from the talks, Ladon had apparently insisted heavily on her presence. This didn't make things any easier with John when he found out.

When she wasn't in the labs analysing the new systems the Ancients had reactivated, she spent her time with Teyla, Ronon or Evan.

Right now, she was sat in the lab scrolling through a screen of Ancient text. "He's back!" Rodney laughed.

Alice poked her head up over her screen to look at him. "Whose back?"

"Sam." Rodney said as though it explained everything. She raised an eyebrow, when she didn't reply Rodney looked up from his screen. "What?"

"Again. Who?" she repeated.

"Oh he's the whale that helped Sheppard and Zalenka find me last year."

"You named it Sam?"

"Yeah. Well it looks like he's just outside the city." Rodney stood up. "I bet you could see him from the main balcony." He ran about the lab pulling things out of boxes. Alice leaned back in her chair watching. "Ah ha!" He pulled out a pair of binoculars. "Do you want to?" he gestured to the door.

"uhh…I'm good. Say hi for me." She smiled, watching as he eagerly scampered out of the room.

Evan was walking through the door, pressed up against the wall to allow Rodney to dash past him. "Afternoon Aly-cat. What's his deal?"

She glanced at where Rodney had just vanished. "Something about whales."

"Alright… anyways, what are you up to?"

Alice sighed, putting her hands on her head. "Research - as always. Why?" she narrowed her eyes suspiciously at him.

Grabbing her hips he swivelled her chair around to face him. "Capture the flag, I need another team captain."

Alice immediately perked up. "Really?" then she hesitated. "wait, what about…"

"He's off picking up Radek and Ronon from the mainland. Then he's off duty. You've got the whole day." He grinned at her eagerly.

She grinned back. "Then count me in."

Alice wiped the sweat off her brow with the back of her sleeve. As always her team had annihilated Evan's a fact she wasn't going to let him live down anytime soon. She'd even managed to land an Intar shot on him.

Evan groaned. "That's going to kill for a week you know."

Alice laughed. "Serves you right. You knew i was always better at this than you." She nudged his shoulder playfully as he winced. The sun had already gone down and the corridors were gently lit. "I need to hit the showers. I'll see you tomorrow okay?" she turned down the hallway walking backwards towards her room.

"Later Aly-cat." Evan waved as she spun around to walk down the hall.

Alice was almost at her door when she heard Teyla call out. "Hello."

"Teyla?" Alice looked around but couldn't see her friend.

"Wait!"

Alice started running towards her. "Teyla!" She turned a corner to see her friend in front of a door holding her head. "Oh my god. Teyla." She grabbed her friend.

"Alice." Teyla looked around, seemingly just taking her appearance next to her. "I am okay. I just…" She looked towards the door.

Alice followed her eyeliner but saw nothing. "Come on, you should go to the Infirmary."

Teyla smiled and shook her head. Her eyes focusing on Alice's. "Sorry. I am just tired. I am fine, really. I just need to sleep."

Alice knitted her brow together, not entirely believing her. But they'd been through so much together. If Teyla said she was fine, then she owed it to her to leave it alone. "Alright. At least let me walk you back to your room."

Teyla nodded and together they headed back towards her room. "How is it going with John?"

Alice sighed. "It's not. We haven't spoken since our disastrous screaming match in front of Elizabeth."

They stopped walking by Teyla's door. Teyla dipped her head, and Alice copied touching her forehead to her friends. "Give it time. You'll figure things out. Goodnight my friend."

Alice gave her a small smile. "Goodnight." She waited under the door slid shut, before continuing on to her own room.

The next morning, woke up with a pounding headache. It felt like someone was trying to drill into her skull through her temples. Looking over at her watch, the digital output read, 4:16am.

Yawning, she pulled her pillow over her head and squeezed her eyes shut. But it did nothing to alleviate the pain. Throwing the pillow and blankets off, she stood up and grabbed her emergency medkit from her pack and slipped out a pack of painkillers. She made a mental note to go by the infirmary later to restock.

Tipping her head back she swallowed the pills. Even though they were strong it would still be about 20 minutes before she felt the full effect. Grabbing her jacket, she headed straight for the Jumper bay. Radek had told her about what had happened the day before and asked her to take a look at a possible navigational glitch. Hopefully it would take her mind off her headache.

When she walked into the bay Radek was already there, plugged into the main control panel. "You're here late." she remarked.

"Huh." Radek almost dropped the tablet. "Oh Alice. What time is it?" he lifted his wrist to look at his watch.

"Go get some sleep. I can take care of this."

"Thanks." He pushed his glasses up his nose. "It's just so puzzling. I can't seem to find any reason why the navigation was off."

Alice stepped into the jumper and held her hand out for the data pad. "I'll take a look and let you know if I find anything."

"Oka-" A yawn interrupted his words and he slumped out of the Jumper and towards the bay stairs.

Once he left, she took a seat on the bench and started reviewing all the test and data Radek had taken during the night, to see if there was anything in there. It was hard to focus at first, but once the painkillers started kicking in, a numb relief came.

The data was everything she expected. Like he said, she couldn't find anything that would have caused the Jumper to divert off course.

She wasn't sure how many hours had passed, before she heard footsteps approaching the Jumper. She assumed it was Radek coming back. "I haven't found anything yet…" She stopped when she saw John appear in the door.

"Oh. Didn't know anyone was here." He said awkwardly.

Alice glanced back at her data pad, letting her hair fall down over her face. "Sorry, do you need to use the Jumper?"

John shuffled awkwardly in the entrance, he seemed unsure whether to step forward or retreat back. Though at least so far they'd managed not to scream at each other. "Uh...Yeah. Gonna check out some whales. Rodney's on his way" John pointed over his shoulder. "- he's just taking some Dramamine but, uh …" He looked at her. "Yeah, we can take another Jumper." He started backing out the way he'd come.

Alice quickly unplugged her data pad. "No, go ahead. I'm done here anyway." She held the tablet protectively against her chest, her head starting to pound again, and took a false step towards John. Then deliberately walking past him. "Uh. There still might be a slight glitch so just take it easy."

"Well, we won't go far. We'll stay within sight of the city …" Alice nodded, and kept walking past him. "... plus you'll be tracking us from the Control Room."

"What?"Alice froze. "Um… I have other-" but John had disappeared into the cockpit. "Okay then." she said under her breath, heading for the control room passing Rodney on the stairs. "He's in Jumper 4." Rodney nodded a thanks and carried on running.

Slumping down into one of the spare control stations, she brought up the city's internal and short range sensors, marking the jumper and the Whales so she could track them both.

"Alight, Alice you there?" John's voice clicked through her ear. A slight pang of hurt resounded through her as he still refused to use his old pet name for her.

"Yeah, I'm here" Her voice was hoarse, quickly she cleared it and focused on the screen. "The whales – or what ever they are - are about a kilometre away, 200m down at your two o'clock position."

"There they are. Should have a visual on them any moment now." She heard Rodney through the open comms.

She pinched her screen, zooming in on the jumper's position. The whales hadn't seemed to notice them yet or simply weren't bothered by it. Then suddenly the dots moved closer to the Jumper and disappeared.

"Where'd they go?" She heard Rodney ask.

"I don't know."

Alice tapped her screen, trying to figure out what happened, when the dot re-appeared right in front of the Jumper. "Geez! They're right in front of you."

"Yeah! We're aware of that!" John sounded annoyed. "What's wrong?"

She listened closer. "Now my head's hurting too." Rodney complained.

"That's not a coincidence."

"Guys, you should get out of there. It could just be the whales' echolocation…"

"I'm pulling back." John confirmed.

Alice put her screen back to the normal view to monitor their re-surfacing. That's when she noticed a large block of flashing dots. "Uh oh." she zoomed in on it.

"Uh oh, what?" John asked.

"You have a large group of whales inbound, they're heading for your position."

"How many more?"

"Dozens. They're only a few kilometres away, but closing fast."

"Rodney?" John said warily.

There was a few seconds silence. It made her uncomfortable. "What's going on?" she asked.

"Your nose is bleeding." John said.

Alice tapped her ear piece twice. "Elizabeth, we need you in the control room."

Elizabeth's reply came instantly. "Be right there."

Alice explained quickly over the comms what had happened. But she must not have been far away as a couple of minutes later Elizabeth appeared in beside her. "What's their status?"

"They're trying to head back away from the whales. Hopefully that will alleviate their pain." Alice's voice was tense, she brought her hand up to rub her temples trying to ignore the pressure building.

Elizabeth tapped the comms button. "John, this is Elizabeth. How are you holding up?"

"Other than feeling like my head's about to explode, I'm fine." John groaned.

On her screen she could still see the Jumper and the Whales circling around them. "I thought we were moving away from them?" They heard Rodney say over the mic.

"I'm trying to, but they're cutting us off." John said impatiently.

Rodney groaned in pain. Elizabeth gripped the back of Alice's chair, leaning in towards her screen. "What happened?"

"The whales are gettin' way too close." he paused. "Crap!"

"John, what's going on there?" Elizabeth's voice was less composed now.

"Rodney's passed out. His ears are bleeding. We've gotta get out of the water."

Alice turned to the side and hit her earpiece. "Carson we're going to need you and a medical team in the Jumper bay asap." She turned back and shared a knowing nod with Elizabeth. A few moments of silence past. "John, are you alright?" No reply. "John?" she asked again.

They watched as the Jumper suddenly went into a steep incline and burst out of the water. "We're out of the water. Rodney's in trouble. Have a medical team ready." His voice breathy.

"Already done." Elizabeth reported.

Alice watched until the Jumper had landed safely within the bay, then both Elizabeth and her stood up to head to the Infirmary. "Keep an eye in those whales!" She yelled back to one of the technicians.

By the time they got there, Rodney and John were sat up in adjoining beds. To her relief they were both conscious and opening their mouths comically wide as though they were trying to pop their ears.

Alice turned back to face Carson and Elizabeth. "Their eardrums have been perforated." He told them.

"How?" Elizabeth asked.

Alice pointed to the screen, Carson moved aside allowing her to bring up a separate frequency chart. "The whales are emitting an intense low-frequency pulse, like a sonar, as well as an E.M field. The combination is very dangerous to humans, particularly in such close proximity."

"It's the whales!" They all twisted around as Rodney loudly shouted at them.

Alice and Elizabeth both exchanged a look with Carson. "Hearing's been impaired. It should heal soon."

"It's their echolocation. It's creating very powerful vibrations. The closer we got, the worse it became." Rodney continued to yell.

Alice couldn't help but smile, she closed the screen and walked over to his bedside. "We know Rodney!" She said loudly.

"Oh!"

Next to him, John was holding his nose and taking in a breath. He looked over to see them all staring at him. "What?" He said as loud as Rodney.

Alice held up her hand to cover her laugh, turning it into a cough.

Carson and Elizabeth joined her, both with concerned looks on their faces.

She patted Rodney's leg. "I'll check on you later!" She pointed at him and then started walking out of the room. "Oh Carson, could I get a restock of pain meds for my kit?"

"Sure love, but didn't you just restock yesterday?" Carson walked over to the dispensary, entering in his code in the door.

Alice rubbed the back of her neck. "Sorry, I had a really bad migraine this morning and had to raid my pack."

His face was unreadable as he handed the meds to her. "Last night? How's it been since?"

"Yeah, it's not really gone away but it's manageable."

Carson handed her the meds. "Okay, but come and see me if it starts getting worse."

She took the tablets gratefully and headed straight back to the control room. The whale pod had grown exponentially in size and were now surrounding the city. "Elizabeth, you need to see this." She called over her shoulder.

Elizabeth came across from her office with Ronon and Teyla behind her. She pushed her chair to the side so the others could see her screen. "The whales are coming from every direction. There are thousands of them. And it looks like they're all heading here."

Elizabeth looked at her confused. "We are their destination?"

"It looks that way. The signals they emit are their way of communicating with each other. Unfortunately, the closer they get to the city, the more it may affect the people living here." Alice frowned, feeling helpless.

"Even above the waterline?" Ronon asked.

Alice grimaced, but nodded.

"We are already being affected. Several of us are experiencing headaches - not as severe as Doctor McKay or Colonel Sheppard - but if these whales get any closer …" Teyla trailed off.

Elizabeth grimaced. "Turn on the shield."

"Yeah…" Alice agreed, rolling over to activate it.

When she turned back around a splitting headache hit her. She blinked, and in front of her she thought she saw two people dressed in Ancient clothing standing at one of the control consoles. "Alice?" She thought she heard Elizabeth's voice, but her gaze was fixed on the Ancients.

They were speaking quickly, their faces looked panicked as they worked on the control panel. She took a step closer, the voices got louder, but it was like all the words were garbled together. No matter how hard she tried she couldn't make out a single word.

The pain intensified, "Aly!" Ronon called. There was a screech and pressure built in her sinuses, head and ears. Then she felt nothing.

—-

When she came to, she was laying under a bright light. Squinting she held up her hand to cover the source, it took her a moment to take in her surroundings. She was in the Infirmary, her head still pounded. Pushing herself up into a sitting position she saw Carson standing over a bed nearby.

Groaning she pushed herself up and swung her legs off the bed onto the floor, heading for the Doctor.

It wasn't until she got closer she realised he was standing next to Teyla, but her eyes were focused off into the distance. Alice turned and almost fell over, where a few seconds ago had been an empty space, was now an Ancient operating theatre with a severely burned man. The pressure started building again. "Alice!" Carson rushed over.

"I'm fine." She turned away, wincing as the headache increased.

"No you're bloody not." He held a piece of gauze up to her nose, Alice hadn't even realised it was bleeding.

"Carson." She chided. Moving towards Teyla's bed. "How you doing?"

Teyla's distracted gaze focused on her for a split second. "I'm fine." Alice winced realised how she unconvincing she must've sounded to Carson not two seconds before.

Alice looked back at him. "What's going on?"

"It's the Whales. The more that arrived the worse you're getting." He took her arm and guided her back onto her bed. "We had to sedate you."

Alice winced. "That bad huh?"

Carson raised a torch and looked into her eyes. "I don't know why, but a few of you seem especially sensitive to the whales." He lowered the torch and that's when Alice noticed all the beds around her, filled with personnel. Some sedated, and others scrunching up their faces in pain.

Before she could reply, Elizabeth walked in and headed straight for them. "I've just spoken with Colonel Caldwell. The Daedalus Infirmary is ready to beam up the sickest of the patients."

"Good. Teyla and Alice should be amongst the first to go." He gave both of them a hard stare. Alice opened her mouth to protest, but Teyla beat her to it.

Teyla shook her head. "No. I'm staying."

"You're far too sick, dear. Both of you." Carson pleaded.

Alice was about to protest, when a rapid panicked babbling echoed behind her. Almost too scared to turn around, she steeled herself to see a man writhing in agony on an Ancient operating table. She pushed off the table and covered her mouth with her hand.

It was like she could smell the burnt flesh of the man. "Aly?" Carson put his hand gently on her arm. But she didn't turn around, she realised the man's clothes looked familiar. Like a flight suit, she'd worn enough in her life to recognise the practical over comfort design. "He's a pilot." She murmured.

"It's a uniform." Teyla's voice behind her, let her know she wasn't the only one to see it.

Alice took a step closer, the pain increasing as she did. "Who is?" Carson asked.

A sharp pain stabbed through her temples. "The burned man." Alice carried on. She pinched her nose trying to alleviate the pain. "He is an Ancient pilot."

Her ears popped and she felt a warm liquid dripping down from them. "Alice." Carson pulled over a chair, so she could fall into it.

She struggled to take in a breath. "I just…need a moment."

"No. No more moments. Nurse." She felt the bed moving underneath her. The pain in her ears intensified, and a warm liquid started dripping down out of her nose. "Colonel Caldwell. Ready to beam the first group."

Her last view was of Teyla and Carson, watching her with concern as the white light engulfed her.

The Daedalus' medbay was teeming with nurses and patients, as they carried in body after body. All of them wore Atlantis uniforms. She lifted her hand to her head, it was only then that she realised a drip had been attached to her hand.

Gently lowering it back on to the bed, she looked around for the head medic. "Doctor!" She called out. Realising that everything sounded muffled and out of focus.

"Doctor Riley." She could see the familiar words form on the doctor's lips, but they barely registered in her ears. "Good to see you're awake."

It was disconcerting to only hear a muffled voice. "I can't hear very well."

The Doctor gave her a reassuring smile. "You perforated your eardrums. You'll be fine in a few days."

Alice just nodded, only catching about half of what he said. "Atlantis?" She asked, realised that she was mostly likely shouting as he winced back away from her.

He just shook his head slightly. "Not good. But I don't know anymore."

Alice closed her eyes to think, the pain in her head was dull. Probably in part to the meds they were pumping into her. But it meant it was clear enough for her to consider their options. To do that she needed a better understanding of what was going on.

She opened her eyes. The doctor had moved onto another patient, probably thinking she'd fallen asleep. Checking to make sure no one was paying her any close attention, she ripped the IV out of her hand and slipped off the bed.

The medbay was so busy with people coming in and out, no one noticed an extra one heading out the door, with a borrowed medical jacket.

She ran down the corridors towards the bridge, as she ran she could feel the vibration of the ship's engines powering up. They were on the move.

Picking up her pace she ran out of an adjoining corridor and straight into John. "Riles?" His arms shot out to catch her shoulders.

Even though her hearing was still muffled she knew exactly what he was saying. It was written clear as day across his face.

"I can't just sit in the infirmary and wait to die." She said, or yelled, defiantly.

John narrowed his eyes and stared at her. All she could hear was the sound of her heart as it pounded in her chest. He was evaluating her, and she knew it, if she showed any sign of weakness now he'd have her hauled back to the infirmary. He was also probably deciding if this was worth the effort to fight over.

"Rodney's in the engine room." He said loud enough for her to hear. She turned to leave but John caught her wrist. "One slip and I'll strap you down in the Infirmary myself."

His tone was serious, but Alice couldn't help smirking. "I didn't realise you were into that."

Without waiting for his reaction, she slipped out of his grip and headed for the engine room.

"Rodney!" She yelled into the room. He was holding a large bundle of cables with crystals attached on either end. One side was still connected to a tray in the wall, whilst he walked the other side over to a makeshift ZPM holder. She froze in place. "What the…"

"Good! I need the extra hands." He dumped a load of the cables into Alice's arms then scurried back to the crystal tray. "Connect those to the ZPM!" He must have said it twice, as it was obnoxiously loud, and he stared at her gesturing to the ZPM.

Alice got the gist, the tray Rodney was messing with was for the shield generator. Whatever he was planning they were going to need a lot of extra energy.

"What, we are already?" Rodney's sudden speech surprised Alice. Glancing over thinking he was chatting to her, she realised his head was still down in the tray, with a finger on his ear. "Aly! Is the ZPM connected?" He yelled at her.

Alice snapped her head back down to the connectors in her hand. "I need one more minute." She worked quicker.

A loud alarm sounded on the wall panel, loud enough for it to make her deaf ears ring.

Rodney's faced paled as he read the screen. "The prominence is fully collapsing into the photosphere. Brace yourselves."

Alice slipped the connectors into the right places and grabbed the ZPM just before the ship started shaking. "It's ready!"

The shaking wasn't horrible, so Alice carefully secured the ZPM. Then walked over to Rodney to look at his read out. That's when she realised what they were doing.

The Daedalus was being used to diffract the solar event away from Lantea. "This is crazy." She grabbed the tablet and ran through the data. She grabbed a radio off the nearby desk.

"How long will this last, Doctor?" Caldwell asked.

Alice replied before Rodney could. "We have no idea. These kind of solar events can last anywhere from a few seconds to several hours." Her eyes widened. Even with the extra power boost from the ZPM, the hull wouldn't be able to last more than 30 minutes.

"Hours?! Rodney! You never said anything about hours!" John barked.

"We're building up serious heat behind the shield." Caldwell said.

Rodney dropped his hands onto his lap. "I told you this wasn't a good plan!"

—-

Rodney and Alice watched the readouts from the engine room. "Temperature inside the shield's rising too fast. I'm already detecting several failed sensors on the bow." Alice reported.

"If this thing keeps going, the heat build-up could damage the hull." Caldwell's voice was tense.

"Not "could." It's already damaging it." Rodney said.

An alarm beeped from the main station. Alice wandered over and checked the screen. "We have a breach in the 302 Bay."

Another alarm beeped. "Another breach. Deck four - we're venting atmosphere." Rodney clicked his finger to Alice, pointing at the next station. Quickly, she set an evacuation order and started sealing off the section.

"Rodney?" John said hesitantly.

"The connection is inefficient." Alice started saying, staring at the ZPM. "Maybe if I reroute-"

But Rodney held up his hand. "It's over." He said so quietly it was almost a whisper.

"And we're not toast." John said excitedly.

"We're not toast!" Rodney repeated in disbelief.

Alice sighed and slipped down onto the deck, wiping a thin sheen of sweat of her forehead.

"Good plan, huh?" John quipped.

Alice shook her head. "That might have been one of the worst."

Once they'd made sure they'd sealed off any section venting atmosphere, they headed back to Atlantis.

Alice stormed towards the bridge, John was just walking off it. He saw her coming and held up his hand.

"This is not the time." John tried to push past her.

She stepped sideways blocking his path. "I'm sorry, but there doesn't seem to be any other time."

"I'm not having this conversation again." He said, keeping his voice low.

"Again?" she shouted. "I must have missed the first time. Why don't you refresh my memory?"

John reached out gripping her arm and leading her away to the side, glancing around at the other personnel watching them. "Keep your voice down."

"Why should I?" Alice ripped her arm out of his grip. "It seems to be the only way to get your attention. You could have gotten everyone killed."

"Well I didn't."

"Yeah you got incredibly lucky." Alice clenched her fists at her side. "You have no idea how close it was."

"And you would have preferred we did nothing?!" John pressed closer to her. "Atlantis is safe, and we're all here. So what is your problem."

"You didn't give us a choice. There could have been a better solution." Alice glared at him. "But you always do this. You make decisions based on assumptions and don't actually think them through." She knew she wasn't just talking about this plan. "You're not always right, and one day it's not going to work."

"Get back to the infirmary. Now." He wasn't shouting anymore. "Get her out of here." A couple of hands grabbed her and lead her back towards the infirmary.

She'd pushed it too far this time.