AN:- New year, new story!

Chapter One: Aite

It was a changed Normandy.

That was the only thought running through Shepard's head as she double checked the latest reports from Miranda. They had lost some more crew, and hadn't gained any to make up for it. She had known it would happen, objectively, and to say they were gone wasn't exactly accurate, but it was still quite melancholy reading.

Kasumi had left them not long after they passed through Citadel space again. Shepard had thought it was just a quiet shopping trip, and mostly she had been intent on replenishing Chakwas' medicine cabinet with some Serrice Ice brandy. But when she returned the lounge was empty of both thief and possessions, with only a datapad left behind to explain her decision.

'I don't like goodbyes,' the final sentence read. 'And we will meet again.'

Legion too was gone, more recently. That she had expected, though it surprised her how much she missed the strange machine. Once he had been fully repaired he had requested her permission to exit the ship, and she had granted it willingly. Although most of the squad accepted his continued presence, Tali somewhat grudgingly, the rest of the crew had been immensely disturbed the first time the geth stomped through the mess hall. More than one had drawn a firearm, and hadn't that been a fun discussion to have with Gardiner?

She was sat at the mess hall table, the lights dimmed, trying to convince herself she wasn't moping. Only that morning Mordin had left them as well. He hadn't disclosed the exact reasons for his leaving, stating that they contained national secrets he wasn't happy discussing, but she had the feeling it had something to do with his genophage work. After the Collector's mission was finished he had spent most of his time locked in the lab tracing gene sequences, and EDI reported that Maelon's datafile had been opened and accessed repeatedly.

"Late night Commander?"

She grinned. No matter the events, no matter how low she felt, Joker somehow always managed to bring out a smile. "Early morning," she admitted. "Couldn't sleep."

"Well our course is all laid in, so there's not much for me to do but relax." He eased himself into a seat and leaned back. "It would be nice to have some real down time."

"Believe me I hear that Joker. We'll have some leave after this mission's done."

"Must be nice not having to ask the Alliance for permission to take a holiday."

She nodded. "Nice to have the money to go on holiday as well." She held up the datapad she was pretending to read. "Found a buyer for all those excess minerals we seem to keep picking up. You'd be amazed what the going rate for eezo is these days."

"Any hints on the price?"

"The entire crew could retire tomorrow and live the rest of their lives off what we've already made."

"Okay so we really are rolling in cash."

"Well not exactly. There's ship repair to consider, which given the Normandy's specs is going to eat a few million away easily. Plus refuelling constantly, cost of more probes, weapons, armour, salaries." She shrugged. "It all adds up."

"That's why I resisted promotion. I like it in the pilot seat. Stars ahead, comfy leather chair, no worrying about excessive costs."

"TIM was kind enough to handle all of this for us before, but since we're effectively independent contractors at the moment I have to take up the slack."

"Let me know if we're gonna go bankrupt."

She grinned. "Just remind me never to start up my own PMC. I don't think I could handle the stress."

He smiled back. "You're the only person I know who can face down a Reaper on foot and still consider paperwork the more stressful thing."

"Well it was only a baby Reaper."

He struggled to his feet and headed for the kitchen. She tried not to make it obvious she was watching as he fished out the coffee and found a clean kettle. He had broken almost every single bone in his body less than a month before, and she wasn't entirely convinced his recovery was really finished, no matter what he said.

"So what is the mission, O Captain my Captain?"

"One last bit of Cerberus business to clear up. Miranda found it on her last search through the datastream. Some sort of project that went rogue."

"That is a bit of a recurring theme around here."

"Well I figured we could use it as some pretty good blackmail material to keep TIM off our backs. Plus it'll put us in good favour if we decide we want back into the Alliance."

He came hobbling back with the coffee. "And do we want back into the Alliance?"

"We want back into anyone that's going to let us fight the Reapers while maintaining some sense of decency and ethical conduct." She went back to the datapad. "Also someone who'll pick up the slack for us monetarily."

"Hey if it helps I won't order the real coffee next time."

"Don't you dare Joker." She took a sip from the mug he had placed next to her. "There will be no galaxy saving without caffeine."

/|\

On a scale of Eden Prime being destroyed by a Reaper to evil Collector Base with a Reaper fetus, Aite was one of the more beautiful planets they had visited. Which definitely contributed to Shepard's massive sense of paranoia about the place. She sat next to Joker as he brought them in through the atmosphere, heading for the coordinates Miranda had found for them. As they followed the curve of the planet Miranda came into the cockpit and leaned over EDI's terminal to check out of the window.

"Pretty," she said dryly as she sat down in the chair behind Shepard.

"What do you want to blow up first?" Joker asked, half-turning to Shepard.

"Thought I'd start with everything." Shepard brought up the data Miranda had found. "This place already stinks."

"It's a secret Cerberus facility. How could it not?"

"Care to weigh in Miranda?"

"The information I found suggested that there was some sort of Artificial Intelligence research was being carried out here."

Joker snorted. "That's always a good sign."

EDI sprang to life next to him. "May I remind you Jeff that my existence is owed to a Cerberus research facility."

"Yeah, and now you're part of our pirate crew. Definitely a success story."

"Pirate is an incorrect term to refer to Commander Shepard and the current alignment of the Normandy crew. The word-"

Shepard cut her off. "Later EDI." She looked back to her monitor. "Distress signal last reported from this facility Joker. You have a landing zone?"

He checked the scan and shook his head. "Nothing big enough to get to Normandy down. You'll have to drop in the Hammerhead."

"Oh goody," Miranda drawled.

"I'm much better with that thing Miranda." Shepard stood and nodded to her. "Let's get ready for drop."

"Who do you want to bring?" Miranda asked as they walked back through the CIC.

Shepard ran through the possible list. There was barely any room in the Hammerhead, compared to the shuttle or the mako, but then she had a feeling they would need the gun. "Tell Garrus to get ready, we'll need his eye on the gun."

"Room for one more then."

"Might as well be Tali."

They stepped into the elevator, Miranda bringing up her omni-tool to issue the muster. "Sooner or later Grunt is going to get bored."

"I've been thinking about that actually." Shepard tried to avoid letting her sadness show. "I think it might be time for Grunt to go back to Tuchanka. He deserves to learn about his heritage and find his place in their society."

"Are you sure Shepard?"

She nodded, trying to avoid Miranda's eyes. "He was never given a chance to do anything other than this. He was basically born on this ship."

"I understand. But we are losing a lot of our crew now."

"We were never meant to stay together. I thought you and Jack would have murdered each other long before now."

It was now Miranda's turn to look pensieve. "She's changed hasn't she?"

"I think so." Shepard glanced over. "Have you spoken to her yet?"

"I have."

"And?"

"And I don't think she's going to kill me."

"Well that's something at least. Did she speak to you about how she's doing?"

"A little. Hasn't she spoken to you?"

"Once or twice. But I don't think she would really share much with anyone."

Miranda nodded. "That does seem a little unlikely. What does Dr Chakwas say?"

"She'll be able to begin walking soon."

"Good. Will she be back on active duty?"

"Not for a while yet." Shepard toyed with the plates on the back of her gloves. "Honestly I think she's going to leave as well."

Miranda frowned deeply. "Why? I thought she had found a home here."

"Thane's death hit her hard. Did you read the report?"

"I haven't actually." Shepard looked at her, surprised. Miranda shrugged a little. "If I'm honest reliving it seemed somewhat morbid."

"According to her report Thane held the husks back while she got away. I think she's having difficulty coming to terms with the thought of someone else sacrificing themselves to save her."

"Can you really blame her?"

Shepard shook her head. Reading her report had brought back a lot of memories of Akuze. "No I don't blame her."

The elevator doors opened and they stepped out into the hanger bay, heading over to where the Hammerhead was dangling in its support struts. Shepard spared a moment to glare at it, then went to check on the repairs. Most of the hull was now patched up at least, which at least meant they could give the shielding a rest, but there was still a lot to do if they wanted to ever get back to full operational capacity, and most of it would have to be done at a real dry dock.

"Maybe I should just take Joker up on his suggestion," she said as Tali emerged from the elevator.

"What suggestion would that be?" Miranda asked.

"Piracy. They'd have proper facilities to keep their ships repaired. Plus I'd actually get to keep some of the booty."

"You keep more than enough of it as it is."

"Fair point."

The elevator opened again and Garrus joined them, wearing the new armour he had found at the Shadow Broker's base.

Liara's base now. Shepard reminded herself. Another trip might be in order soon.

"Alright people. We don't know what we're walking into over there, so be alert for anything. We all remember what happened the last time we went up against an artificial intelligence."

"ETA five minutes Commander."

"Everyone into the Hammerhead."

"You want me to drive?" Garrus asked as they piled in.

"Very funny. Get on the gun, I'll show you how it's done."

/|\

"Ow."

"Stop complaining Tali. It wasn't that hard a knock."

"Just a suggestion Commander, maybe next time you should engage the thrusters a little before we've already hit the ground."

"Stow it Vakarian."

As they approached the landing zone for the facility the comm crackled to life with a man's voice. "Thank God you came. My name is Doctor Gavin Archer. The situation is urgent. We're facing a catastrophic VI breakout." He sounded genuinely distressed, as much as she could tell over a radio link. She wondered why he wasn't using a more up to date method of communication. "I'll explain the details later, but you must retract that transmission dish. The controls aren't far from your position, you have to hurry."

They piled out of the Hammerhead and raced inside to find a regular sterile-looking Cerberus facility. It was identical to every other pre-fab she'd ever seen, aside from the lights not working and the smell of blood and burned bodies everywhere.

"Something bad happened here."

"Quiet down Garrus." To the left she could see a stairwell, smoke rising from it. "Miranda up front. Tali support. Move out."

They fell into silence as Miranda and Tali led the way down the stairs. There were two bodies halfway down, one with a dozen bullet wounds to the torso, the other with a hole the size of a dinner plate burned right through him. The weapon, whatever it was, had left a burn on the wall behind him as well, and the smoke was rising from it.

"Over here on the monitor." It was the doctor's voice, coming from one of the banks of computers below them. Shepard marched past a fire still burning on the floor and leaned down to see a balding man with a five o clock shadow. He looked dishevelled and exhausted, but his voice was clear and confident.

"Ah, there you are. I've locked myself in a computer room on the far side of the base. There are geth on the loose. A rogue VI program has seized control." He briefly looked away from the screen. "I've lost a lot of friends today. I'd hate to see you join them. Please watch yourself."

The communication cut out and she looked over to see Tali and Garrus working at the door.

"There's no way out of here," Tali reported. "This door… it's like nothing I've seen before."

"What do you mean?"

She stepped back and kicked the door. "It's locked, but not in any way I've seen before."

"That's not comforting." Shepard looked around, trying to spot an alternate route. She spotted a body on the floor beneath one of the windows, riddled with bullets. The window behind had been almost shattered by the gunfire. She drew her pistol and walked round the desk, shielding her face and blasting through the glass. "Come on people."

They jumped through into the small adjoining room, where they found an open door that led them into a corridor beyond.

"Found a personal log," Garrus said softly. She walked over and activated it.

She identified the voice as the same man they had just been talking to. "Archer's log: status report. Please inform the Illusive Man that we've made great strides in our research. His doubts about the lack of progress were unwarranted. A demonstration is forthcoming."

"Because that sentence can't ever be followed by something bad," Garrus drawled.

Shepard didn't even bother responding, moving to the door and checking down the corridor. The entire facility seemed to be deserted, which set her teeth on edge. Something had to have caused the massive destruction here, so why had it disappeared immediately afterwards? The only logical solution was an ambush.

Through the next door was an obvious control room, a massive window taking up an entire wall and showing a gigantic satellite dish beyond. There were more bodies scattered around here, one by the door as though he had tried to run, another slumped at a bank of computers. Shepard paused in the doorway and scanned the room but saw no obvious traps or signs of sabotage.

"Check it," she said, and her team moved past her and into the room, sweeping it completely with omni-tools. Only when Tali had finally declared it clear did Shepard enter after them.

"Got another log here Shepard," Garrus said. "Same ID tag."

"Play it." She wanted to know more about the sole survivor of this whole operation. In her experience sole survivors were either extraordinarily lucky, or they engineered their own escape at the cost of everyone else.

"Memo to all project personnel. I understand there are some concerns about handling live geth. I agree it's a risk, but the potential rewards are far greater. Someday your sons and daughters will thank you."

"They had live geth here?" Unsurprisingly it was Tali who seemed most concerned with that revelation. "What were they thinking?"

"Standard Cerberus Operating Procedure," Shepard said. "They weren't." She moved to the central controller and activated the satellite dish controls, retracting it. She looked up to make sure it was working when the entire window suddenly glowed green before her, blank staring eyes that fixed on her as a binary scream hit her like a concussion grenade to the face. She doubled over and pressed a hand to her forehead.

As quickly as it had come the sensation was gone and she was able to hear the concerned voices of her teammates, overlaid with Dr Archer's panicked chattering.

"Dammit, the VI's overridden the controls. We have to stop him, he's trying to upload his program off planet. Destroy the antenna inside the dish, there's a tram on the lower level, get to it as fast as you can."

She nodded, stepping back from the console and turning to find her squad staring at her.

"What's wrong?"

"You just keeled over Shepard. What happened?"

"The eyes? That scream?" She saw confusion on their faces and felt cold worry seep into her. "You didn't see them?"

Tali shook her head. "You tried to retract the dish and a computer error flashed up, but there was nothing unusual about it."

"Right." Shepard reflexively clenched her fist. "That's not encouraging."

"What did you see Commander?"

"When I tried to retract the dish there was a scream, like a geth or a Reaper, and I saw green eyes on the screen, looking at me."

Miranda and Garrus exchanged a look. "What?" She asked.

"Archer said that the AI was affecting computer programs in the area," Miranda said slowly. "And there's a lot of it in your head…"

Shepard took a deep stabilising breath. "So you're telling me I'm at risk of being overridden?"

"For lack of a better word." Miranda shrugged helplessly. "This wasn't ever a scenario we anticipated you'd need a defence for."

"Alright then." An odd sense of calm had replaced the worry. "That makes things simple. We have to destroy that dish and shut down the AI before it gets off world and before I lose control. We've handled worse." She moved across to the other door, drawing her SMG. "Form up. Let's go."

AN:- This really will not be such a big update. I've already got the first three chapters and the epilogue written, so there's literally only one chapter left. I just thought I'd get the whole thing out of the way in one go to cleanse the palette for Arrival.

'There will be no saving the galaxy without caffeine.' This isn't taken from anything. But after the amount of times I've mentioned or referenced coffee and the crew drinking it or complaining about military issue coffee while Joker has the 'real stuff' I thought I needed to throw in a reference to how much it gets mentioned.

'Pretty. What do we blow up first?' That is taken from somewhere. (all together now) X-Wing Wraith Squadron books! It's the motto of Wraith Squadron. Since it migt as well also be Commander Wedge Antilles Shepard's motto I decided to throw in (yet another) shout out.

The biggest change to my writing of this whole mission is probably Shepard's reaction to the VI. In the game it's basically made clear that everyone can see both it and its effects (like the green hue surrounding the geth when it controls them) In the story, only Shepard can see and hear it.