Note: Thanks so much to those that reviewed the first chapter! Let's me know you're still interested in this story! And yay, alt!Raph is back! :)

Dis: I don't own TMNT

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Tate:

"Maybe we should get you checked out."

Tate Jenkins ignored the officer's concern while being escorted to the lab. He could taste the blood from his busted lip and feel the ache in his shoulder. His leg hurt like a bitch, something he hadn't felt with the adrenaline in his system while in combat. Still, he needed to get these disks to… What was her name again? Molly? That was his top concern and honestly he'd had much worse injuries before.

"Just get me to the lab," he said. "These disks are more important than a busted up shoulder and a leg wound."

The soldier nodded and Tate followed him down a corridor with only a slight limp. It was a wide hall with numerous doors, the red light above the keypads indicating that they were locked. Upon coming to a large sliding glass door, the soldier brought out his I.D. badge and scanned it. Dual doors slid open with a soft whoosh and Tate's blue eyes traveled around the room. He'd been in Donatello's lab once and it was twice the size of this one but it seemed both Donatello and Molly had an affinity for junk. Piles of scrap littered one table; mixed technologies of different races tangled together by the wires and bent metal. On another table was a disassembled Triceraton stungun and next to it was a disassembled Triceraton assault weapon that could blow holes in your chest. He'd seen it done on the cadet that had been standing beside him just a few hours ago. Shaking away the wisps of the past that threatened to entrap him he turned away from the table as a loud clank filled the room.

"Dang it!" hissed someone from behind another table. This one had a few stacks of papers, an open laptop and a mug of steaming coffee sitting untouched on its surface. "Great! Just great!"

"Dr. Hilde?" asked the soldier behind him, earning a startled squeak as the woman popped her head out from behind the table. THIS girl was a Doctor? He had to wonder how old she was because her face looked incredibly young. Nineteen? Twenty? Not much older than that. Her eyes were a darker shade of blue than his and her hair was shoulder length and a dark brunette. Images flashed behind his eyes of a woman that looked similar to her, on a swing set, laughing as she kicked her legs-and once again he had to shake away the past.

"Hey! Hi…" She stood her full height. She wore a simple gray sweater, the collar of the white button up beneath it folded neatly at the neck along with the cuffs at her wrists. She had on black slacks and black shoes that looked polished. She picked up the device she must have dropped and set it on the table before pulling a strand of hair behind her ear nervously. "Thomas. Good evening."

"Ma'am," said the soldier that had brought him down. "This is Lieutenant Jenkins."

Tate nodded as she looked at him curiously. He reached up into his vest and pulled out the data disks. The way her eyes lit up brightly let him know they truly were important and he offered them to her. He had flecks of blood on his hand and dirt under his nails but she didn't hesitate to snatch the disks. Immediately she rushed to another computer. She put on an ear piece and within moments there was an image of one of his two Commanding Officers on the large screen on the wall. Immediately he stood straighter, hands going behind his back.

"Dr. Hilde," said Donatello, eyes drifting to meet Tate's for a moment. "I see my operative made it to your lab safe and sound."

"Indeed he did," she said, holding up the disks. "These are Triceraton date disks but something looks different... I don't recognize the writings on them."

"Will they interface with the Triceraton drive?"

"I… I think so."

"Excellent. Remember what I taught you?"

"Of course," she said, walking to another table, all eyes on her as she opened up a tray. "The salvage team brought this drive in just last week. The other one we had overloaded."

Tate's eyes watched as she snagged her laptop and connected it to the device which was now glowing gold. Within moments the screen on the wall split. Half of it was Donatello's face and the other half was-Something. Code? He didn't recognize any of the symbols. Honestly when it came to the workings of any of the technology he used or was used against him he was lost on the specifics. He just knew how to use it. And he knew how to use it well.

"You're free to go and get that leg checked out," said Molly, fingers tapping over the keyboard of her laptop, taking a brief moment to meet his eyes. "This could take a while, even with the translation program, not to mention the unknown language-plus you're bleeding on my floor and I don't much like it."

Tate looked down and sure enough there was blood on the floor. Wincing he gave her an apologetic look, but she was already looking back down at her laptop. His eyes traveled to the main screen and once again he stood straight. His general was looking at him with a bit of sympathy. Donatello knew what he had gone through that night. Knew what it had taken to get those disks back into home base.

"Dismissed. Get looked at. I'll arrange transport for you back to base three and we can debrief when you arrive."

"Sir," said Tate, saluting. He was halfway out the door before Molly spoke up.

"Lieutenant?" He looked over his shoulder, blue eyes pained, and not just from the wounds on his body. She fumbled for a moment, not expecting the emotion he was showing, and he slammed his walls down. It had been a mistake; he was so damn tired and ready to just forget the entire day. "Thank you."

He nodded before stepping out of her lab. The doors closed behind him and he followed his escort to the Med Labs. The man on duty was shorter than he was, and more rounded in the middle. Half his face was covered by large glasses that magnified his brown eyes which had crows-feet etched in the corners. His red hair was thick and covered his head, cheeks, and jaw. He wore the traditional white lab coat and his I.D. card said Dr. Henry Milton. Within moments his leg was numbed, stitched, and bandaged. His other wounds were quickly tended to, and he refused to wear the sling because it wasn't anything but a precautionary measure. He could move it just fine and it wasn't like he had dislocated it. His clothes had been ruined so new ones had been dropped off. He slipped on a pair of sand colored cargo pants, which sat low on his hips due to being a little too big. He strapped on his belt to keep them up, his weapon secured at his side. Finally he pulled on a black, long-sleeved top that clung to his arms and chest: covering the dragon tattoo that curled around his right bicep. He winced as his shoulder pulled slightly and ignored the glare from the doctor as he strapped on his vest and put on his boots. He snagged his visor and gave a quick salute to the doctor before leaving out the door. Jake was on the other side and the mutant lizard nodded at him before taking the lead back to the elevator.

"How's the leg?"

"Its fine," said Tate.

"Got yer room set up for ya," said Jake, entering the elevator and pushing a button that was two levels higher than Alice's.

"How's the girl?" asked Tate curiously. "Gotta be one hell of a shock being back here."

"She's managing," said Jake.

"So you knew her? From before?"

"You sure ask a lot of questions," said Jake, shifting from foot to foot. "And yeah. I did. I was part of the team that picked her up when she arrived here the first time."

They continued downward in silence. Tate leaned against the back wall of the elevator easily, taking some of the weight off his leg in the process. Maybe he should have gotten some pain pills from the doctor, but he sure as hell wasn't going to go back for them. He had pride, and he definitely had worse done to him before. He chanced a look at the lizard mutant, over the hard crown of bone atop his head to the scales that gleamed green, blue, and red.

"So why are you here?" he asked calmly. "And not at Base Two?"

"Same as you," said Jake shortly. "Had a mission, ended up here, Raphael went out with Siren and I decided to stay and keep the king's throne company while he was gone."

Tate just left it at that and when the elevator doors opened he walked out. Jake remained in the elevator and as the doors were about to close he put his arm out the stop them. Tate hesitated at his assigned room as Jake spoke, a serious look on his face: a look of a man who knew what it was like to go to hell and back.

"You did good, Kid."

Jake stepped back, the elevators closed, and Tate was left alone in the quiet hall with nothing but the sound of his breathing to keep him company. It wasn't until he was locked in his room that he felt comfortable. He pulled off his gear once more. Visor and weapons went on the small table, vest and boots on the chair beside it. He pulled off his borrowed shirt then went to the bathroom, bare feet padding on the floor. He flipped on the light and stared hard into the mirror over the sink. There was a small towel so he twisted the knobs of the sink sharply then ran the towel under the clear spray. Slowly he cleaned away blood and dirt, permanently staining the towel. He tossed it in the wastebasket when he was done and turned off the water. He looked up at the mirror once more, watching as droplets of water ran down his face.

It played like a movie in his head, over and over again, the sounds of screams and explosions around him. Marty, that had been his name, shouting that they needed to leave before there was a hole the size of a basketball in his chest. He had to get the disks out of Marty's pockets. Tate still remembered the warmth of his blood on his hands. He had escaped just as Triceratons swarmed the room, jumped out a window and fallen with shards of glass to the street below. That was probably when he sliced his leg open. He had hurt his shoulder after landing on the burnt remains of a car. It had taken him a moment to get his breath back and when he'd been able to slide off the car the Triceratons had been there. Shortly after the light had come and it had been that light that had saved his ass.

Stepping away from the mirror he flicked off the light and went to the small bed. The springs protested as he settled in. Pulling his hands behind his head his unblinking eyes stared up at the cracked ceiling. He wasn't sure if sleep would come. His body and his soul hurt and FUCK he would have loved a shot of anything in that moment-or a fucking pain pill. He was certain it would be the shot he'd need most tomorrow. Not only would he have to face his disappointed comrades and C.O.'s, but the broken family members of those that perished on his watch. When he finally did drift off the sleep, his waking nightmares followed him into his dreams.

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Alice:

Her eyes opened, blinking lazily as the morning fog slowly cleared. Smacking her lips she sat up, pulling strands of her hair out of her face. Grabbing her phone she frowned when she saw she drained most of the battery and she turned it off. Yawning, she slid out of bed and did her morning routine. She slipped on her signature black tank-top, a clean pair of brown pants, and zipped up her black boots. She was just pulling her hair up into a ponytail when there was a knock at her door. She opened it and standing on the other side was Jake.

"Mornin' Princess," he greeted. "Ready to get your day started?"

"Good timing, I just got up a bit ago."

"Decided to give you till noon to sleep in, what with the welcoming you had." She followed him easily to the elevators. "We'll get you to Molly's lab first. Get you into the system so that you don't need me to open a door. We'll also get a communicator up and running for you. All the top-ranked personnel have them."

"Are there civilians living here?" she asked.

"Not a lot," he said. "Significant others mostly: and only a few children. We're not a refugee camp. Those that don't want to fight run north into the woods."

"You just send them on their way?" asked Alice. "Defenseless people?"

"There are many havens they can run to," said Jake. "We don't have the resources to house everyone here or at our other bases. The havens in the woods have so far been undetected by the Triceratons. There are about twenty-eight of them. They were first established when Shredder had control of this area."

"But they are technically on their own," said Alice.

She wasn't sure how she felt about that. She remembered how much Michelangelo had loved his people, how proud he'd been to help civilians. Raphael had gained the trust of the people who had been ruled under Saki. Did he just toss them out in the cold when things got tough? True, from what she's seen, this facility was small: but there was no way in hell she could believe they would just ignore the pleas of their people for aid.

"You've seen what it's like out there," said Jake, pressing the elevator button and soon they were ascending to the higher levels. "As I said the havens we send them to were from when people were hiding from Shredder. It was Michelangelo's idea. We gave them the tools to survive, and it's up to them to use them until we win this damn war."

Alice didn't say anything else. She just followed Jake to the labs and as the glass doors opened she was greeted with the sight of a woman drinking the largest cup of coffee Alice has seen in her life. The woman was tall, but had a slim frame. Alice was certain that if she conjured a wave of air the girl would fall over. Upon seeing them she smiled brightly, setting the mug down.

"You must be Alice."

"Yes," said Alice, taking the hand the girl offered.

"I'm Molly Hilde," said Molly, gesturing to a small table that had a few devices that made Alice a little uncomfortable. Mostly the thing that looked like a mini-gun. "Let's get you set up, shall we? Have a seat on the stool this should only take a few moments."

Molly tapped a few keys on her lap top and asked a few, basic questions. Name, birthdate, and past illnesses or surgeries and Alice felt like she was in a doctor's office. Molly held up a tablet and Alice placed her hand on it when asked and Alice remembered the small, cylinder rod from when Donatello scanned her the first time. It scanned her from head to toe, focusing on the eyes.

"We have your fingerprints, retinal scan, and now can you say a few sentences for me?" asked Molly.

"Uh… Like what?" asked Alice.

"Anything," said Molly. "Just so that I have a voice pattern for the recognition software."

"I'm Alice, I'm a Taurus and like walks in the park and think hot dogs are delicious," said Alice. Molly's lips pursed in a smile as she held up the small device that Alice deduced was an injector of some sort. Alice put up a hand, leaning away from the woman with what she considered a weapon. "What's that for?"

"It's a chip," said Molly. "Everyone on the base has one."

"No," said Alice. "I don't need a tracking chip in me."

"But… It's mandatory," said Molly. "If someone is lost or injured on the field or if something were to happen here its the best way to track-"

"I said no," said Alice sternly, and Molly's eyes drifted behind her to Jake. Jake must've given Molly a signal because the woman set the injector down, clearing her throat in the process. The woman pursed her lips in distaste, not liking having to break protocol. She picked up something else. It was a small, rectangular device and she handed it over to Alice. "What's this?"

"A communicator," said Molly. "The password is 1-2-3-4 until you set up your own preference. To turn it on you just tap it."

Alice did that and after hitting her password she saw the home page. It had three icons. The first was an icon of a human and upon clicking it there was a list of six names in alphabetical order: Donatello, Emily, Jake, Michelangelo, Molly, Raphael, and Tate. Going back she saw a cog and clicked it to see the settings. The final icon looked like a power button.

"Don't click that one yet," said Molly. "That is the self-destruct button. When you hit it you have thirty seconds to enter your password before it explodes. It will send a signal upon detonation, indicating your position at the time. It's saved a lot of lives."

"Don't suppose I could get my playlist on this thing, huh?" asked Alice with a smirk.

"On the contrary, if you go into settings and hit 'sync device' you can create a file on the home page and have your files imported."

"Oh… Well that's useful," said Alice. "How do I charge this thing?"

"There is a charging port in your room," said Molly. "It's located on the side table. You just put it on there and when it starts to glow red its working, and it will glow green when fully charged."

"Lovely," said Alice, pocketing the device, the urge to call Raphael hitting her hard.

"I took the liberty of inputting the numbers of those you know in there. Mine is in there mostly for tech support or inquiries," said Molly. She then tapped a few more buttons and the sound of something printing had Molly leaving then coming back, handing Alice a card. She took it, the plastic still warm against her palm from the machine. "This will get you in and out of doors. You have the highest clearance in the place so you shouldn't run into any problems."

Was there a hint of bitterness? Jealousy? Apparently Molly didn't like being told where she could and could not go. Alice pocketed the card with her communicator. Jake motioned for them to go and Alice was more than ready to leave the lab. They went to the elevator and Alice made use of her card. It worked like a charm and soon they were headed to what Jake deemed the 'floater level' where people went about their business on downtime. There was a gym, firing range, hand-to-hand training area, and the mess hall. Alice's stomach rumbled so Jake made their first stop the cafeteria. Alice took a bruised peach and a bowl of chicken noodle soup. There were bottles of water and she snagged one before joining Jake. She felt curious eyes on her and she ignored them, calmly biting into her fruit.

"They're very curious about you, Alice," said Jake. "Your story passed all through New York. Even those that weren't there know almost every detail of your role in taking down Shredder."

"Great. Living legend," she muttered, taking a sip of water as someone slid in beside her. She turned her head and smiled upon seeing who it was. "Tate!"

"Alice," he said, biting into an apple. "How goes the first day?"

"Great," said Alice. "Though I'm sure I'll hear it from somebody about not agreeing to be monitored twenty-four-seven."

At Tate's inquiring look, Jake chimed in. "She refused the chip."

"Didn't know you could do that," murmured Tate.

"I decided that I didn't want to get a fireball thrown at my head and let her have her way," said Jake, stabbing what looked like a piece of meat.

"Right," said Tate. "Good move."

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Alice was back in her room. There really wasn't much for her to do. She had gone with Tate to the training mats after the mess hall and upon his request showed him how she could make and manipulate fire. He was even more impressed when water materialized in her other palm. She had snared the attention of many in the room and for a few minutes had put on a show for them before killing the flame and shooting the ball of water into Tate's chest: which had earned laughter all around.

"Payback is eminent," he has said, pointing at her with a grin that didn't quite reach his eyes. She could see the limp in his step and the sorrow in his eyes. "Now if you'll excuse me, I do believe I have a flight to catch in a bit."

"Yo, keep in touch," said Alice offering a hand which he took. Hands clasped he pulled her in in a half hug, patting her back in a way that let her know he didn't give out hugs much. Hell, neither did she. "I got your number. I'll send off a message later so you have mine… I don't know too many people here so…"

"That's not stalkerish at all, already having my number," he said with a grin, making her eyes roll.

"Molly gave it to me. I could always erase it," she said.

"Ouch, Red, that hurts."

He gave her a mock salute before exiting the training area. Alice had followed soon after, going to the elevator and entering the floor her room was on. On the ride down she took out the communicator, thumbing the smooth surface in thought. She opened the contacts and her anxious eyes traveled over the names. Which to reach out to first? She jumped as a new message popped up on her screen and upon seeing it was from Jake she opened it immediately.

Forgot to tell you. Raphael completed his mission. He'll be back here by tonight.

A smile spread over her face and as the elevator doors opened she made up her mind. She selected Donatello, Mikey, Raph, and Emily and wrote out the message, biting her lip in concentration while her fingers slid over the unfamiliar device.

This is Alice. I'm safe.

What else could she say? Apologize to them for thinking she was dead? Make a joke or insert a customary smiley face? Those two sentences would have to suffice until she talked to them over the communicator or face-to-face. Almost immediately there was a response from Donatello.

Happy you're back. We will talk soon. Emily says hi and will call you later tonight or tomorrow.

Then her communicator was ringing and once again she smiled, eyes lightening to a sky blue as the name on the screen flashed over and over. She slid her thumb to answer and brought the communicator up to her ear.

"Hey you," she said.

"Alice," he whispered. "Is it really you?"

"Yeah," she said. "It's me."

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Siren:

Siren tensed as a small beeping sounded behind her. She turned her head to observe her C.O. He remained sleeping, slouched against the wall, communicator in his hand. He'd gotten a message but she wasn't about to wake him up to tell him that. He was, for once, sleeping soundly: and she wasn't about to wake him up. He barely got enough rest as it was and he could ream her out for letting him sleep later. If it were an important alert, they'd have all gotten the message. What he received was private, and could probably wait a few more hours.

She turned her head back toward the outside, the sunlight that beamed in through the wooden slats highlighting the numerous colors in her hair. Her violet eyes narrowed, the pierced eyebrows scrunching as she took note of yet another Triceraton patrol down the block. Instinct had her gloved hands tightening around her weapon and holding her breath until it was out of sight.

Damn lizards. They were giving aliens a bad name. Siren was part of a small group that had been serving under Saki upon his reign. Her people, the Ukari, were shape shifters by nature. Her natural form was equivalent to the stereotypical image humans had of aliens years ago. Ch'rell had decimated her planet and only a few had been allowed to live and serve under him. She had excelled in battle tactics and had immediately been put upon Leonardo's team after graduating the training program. After the fall of Leonardo and Saki she had wondered what her purpose would be. She had been worried about prosecution but instead Raphael had offered her a pardon and when the Triceraton Army and their allies started to attack she immediately signed up to fight. She made an oath and has yet to regret it.

She liked fighting, the rush of blood and adrenaline: the absolute fury . She has killed many and knew there were more that would die at the end of her dagger or by a bullet from her gun. The humans had a name for what she was:

Berserker.

Yet now, leaning against the wall with faded wallpaper of a floral design, she had a sense of calm about her. Yes she was on high alert due to the patrols, but she didn't have the need to rip someone's throat out. Which was nice, for a change, but she knew that all in due time she'd have that familiar itch. An itch she only acquired through the trainings of Shredder and Leonardo.

She sighed, amethyst eyes focusing once again on the streets below where the skeletal remains of cars resided along with fallen debris from neighboring buildings. Nothing but random pieces of trash or dead vegetation traveled the concrete surface below but she refused to let her guard down. Not until they were safe and sound back at base. She owed Raphael everything, her life really, so she would stand watch over him until the last few rays of light dissipated.

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Alice:

"Michelangelo," murmured Alice. "How are you?"

"A hell of a lot better than I was thirty seconds ago," he said seriously. "How?"

She knew what he meant so she told him everything. From meeting other versions of the turtles to the Time Lord, and finally her journey home. She left out the drama of her love life, and instead opted to skirt around the truth, which was being given an assignment by the powers that be.

"You have any idea what this evil is?" he asked.

"No, but it must be bad enough to warrant sending me back here," she said softly. "Although, I was going to come back regardless."

"Were you?" he asked.

"It would have hardly been fair to make you all think I died," she said, playing with the edge of her tank-top. "I'm still getting the hang of the whole time-travel thing. It wasn't eight months for me. Tell me, how did the Triceraton's take over so quickly?"

"Some of the races of aliens weren't happy about Raphael taking over," said Michelangelo. "They were promised land and slaves and instead were being told to join in rebuilding New York or leave. Those that opposed to the idea joined forces with the Triceratons. The attack was sudden and we were all taken by surprise. Raphael had been in a meeting with the newly elected President of the United States and blames himself for not being there. Remaining forces fought like hell but it wasn't enough. We got locations of secret bunkers not even we knew about and since then have been using them along with a few other key locations to strike against the enemy."

"So that's why you keep your bases free of civilians," said Alice. "You're afraid of moles."

"It's dirty, I know," said Michelangelo. "I hate refusing shelter to those that need it most but what we're doing is important work. Those at the civilian camps are well… Let's say they know how to weed out the moles just as well as we would here."

Alice felt her stomach clench at the idea. "Can we talk about something else?"

"Okay," he said, but they remained silent for the most part. "I'm going to come see you as soon as possible."

"I'm fine," said Alice. "Please trust me?"

"I do… I do…" He sighed. "But I still want to see you."

"I want to see you too," said Alice honestly. "I've missed my friend."

A heavy silence remained between the two of them. She hadn't put emphasis on the word friend but she might as well have. She bit her lower lip, nervous as the silence dragged on. He took a few breaths before answering her.

"And I've missed you. I need to get some things done here now before I leave. I'll… See you soon. Okay?"

"Okay. Goodbye." Click. Alice scowled at the communicator, tossing it aside. "Well, that wasn't awkward at all…Way to go Alice."

She fell back against the pillows, suddenly tired. She needed to have a long, serious talk with Michelangelo. She didn't want him harboring any feelings for her and she knew he couldn't help how he felt but perhaps the talk would help him in some way. All she felt was friendship for the turtle. She didn't have the feelings for him like she did Raphael. Then again even the feelings for the older, more ragged version of her love were just as complicated.

"Maybe I should just forget the whole relationship thing… Yeah… That would probably be for the best…"

Alice must have drifted off to sleep with her thoughts because the next thing she knew there was a pounding at her door. Sitting up she rushed to it, thinking it was Jake with important news. She whipped the door opened and there, standing on the other side in his tactical gear and panting as if he'd just ran a marathon: was Raphael.

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TBC…