Ok, this has actually been sitting in my folders for a couple months since the begining of summer, with another couple of fics of mine, but now that I've updated all of my Digimon fan fics I don't feel guilty about posting them now! :D

This fic was inspired by and based off of copperbadge's fan fic, "Coulson's Eleven" and this Tumbr gif set by assvengrrs. After I saw X-Men: Day's of Future Past the idea for this fic just wouldn't leave me alone, so I revised and altered a previously plotted out crossover I'd been working on since first reading copperbadge's fan fic.

I've also been on a Supernatural kick and read a REALLY great Supernatural/X-men crossover that had a great Dean Winchester and Logan/Wolverine friendship called "Wolverines, Wendigos, and Winchesters" by SciFiNutTX, so I decided to throw Dean Winchester in here as well. You don't really have to know or have seen Supernatural to get his part of the story (though it may help), because it's an AU-Alternate Reality for everything to do with the show, and we'll just be dealing with mutants instead of demons and angels, etc. Instead of being raised as supernatural hunters by their father who is obsessed with hunting down a demon that killed their mother, Dean and his younger brother Sam are raised to be anti-mutant and their father is obsessed with eliminating the "mutant menace" and hunting down the mutant responsible for his wife's death.

Ok, enough of that. For more specific information about the fic world, see the notes at the end of the chapter. I explain how different and/or similar movie canon events are for the Marvel movies. I hope you enjoy the fic and please leave a review! :)

Prologue

Originally, it began with an idea. One that would bring together a small team of heroes that would ban together to fight off the threats to our world when we needed them most. Originally this team of heroes started out as individuals that hardly ever played well with others. They didn't get along right off the bat, but they got it in the end. They became a team. A team that our whole world knew. A team that the whole world depended on in our darkest hours. A team that would be one of the first to speak up for mutants when the Sentinels were activated. A team that would be the first humans to die when the Sentinels went rouge and nearly destroyed humanity; normal, altered, and mutant alike. Originally, it was the deaths of the Avengers that brought mutant and normal humans together, made into martyrs.

But then time was altered and it changed everything.

Now it begins with the assassination attempts on Bolivar Trask. Now the whole world knows about the existence of mutants decades before it was originally public knowledge. The whole world began to keep an eye out for mutants the way Americans kept eyes out for Communists during the Cold War. The people of the world over were concerned about the undeniably possible threat that mutants present to humanity, but most were reassured by the presence of one Charles Xavier and his school and his X-Men. The world got an early team of superheroes and look to Xavier Academy with a combination of intense scrutiny and hope. Most of the world is pacified in seeing these mutants aiding their governments. In fact, most countries send some of their own mutants to Xavier Academy for training. There is a sense of peace.

Originally, SHIELD was formed as a result of World War II, founded by influential members such as Agent Peggy Carter, Howard Stark, and Col. Chester Philips, with the purpose of aiding the United Nations in maintaining world peace. Their objective was to prevent international disaster before it could ever reach the scale of another World War. Originally, it worked. SHIELD did it's best to maintain world peace and brought together the Avengers even though it's members Captain America and Black Widow would be the ones to discover it's Hydra faction and brought the Agency down. Some once speculated that the Sentinel Program wouldn't have been initiated if some part of SHEILD had been allowed to remain an active part in global security.

The SHIELD Agency of this new timeline is charged with keeping an eye on the known and suspected mutants and inspects the goings-on at Xavier Academy, as part of their objective in maintaining world peace. SHIELD has their own agents that supervise every government sanctioned X-Men mission. SHIELD, however, also formed a division to continue Trask's research from the confiscated work they seized after the man's arrest. They prepared for the possibility that mutants will turn on humanity. They look into ways to contain them. Charles Xavier himself even lends a hand into helping build prison cells meant to contain the more violent mutants.

For almost 30 years, the world is at peace. Mutants have become bolder and are more willing to revel themselves to their communities and use their powers to help. There are Mutant Rights activists in numbers right up there with those who support Women's Rights and Same Sex Couples Rights. Mutants are now considered a minority. Their number grows yearly, but still only making up a tiny fraction of the global population in comparison to the number of normal humans. Xavier Academy has been expanded over the years to house nearly 500,000 students ranging from ages 8 to 18 from all over the country and other nations. Some colleges have even formed sororities and scholarship programs for mutant students.

But things start to change in 2000, when Magneto resurfaces with his Brotherhood. The X-Men neutralize the threat for the time being, and SHIELD manages to cover the incident up as a training exercise for the X-Men, but SHIELD is on its guard now. Technological genius Tony Stark is brought in to help build more secure prisons for mutant criminals.

Then in 2005, house fires killing young mothers start to become a thing and SHIELD and the X-Men try to find the psycho-pyro-killer mutant that has to be responsible, but it only results in the recruitment of Kurt Wagner for the X-Men, and a young boy, John Allerdyce for the school, but neither Kurt nor John are the cause of the fires. There are no further leads, and no way of predicting where the next fires will occur until they suddenly stop and there are whispered rumors among the mutant community that a strong mutant referred to as Yellow Eyes has been stopped. SHIELD is aware that Xavier knows something, but the man isn't forth coming with the news. SHIELD has to put the issue on the back burner, however, when Victor Van Doom makes a very public attack in New York and the new team of superheroes known as the Fantastic Four come into play at the same time that Magneto and his Brotherhood strike San Francisco in order to destroy the source of a developing serum that neutralizes mutant genes and abilities. Both Magneto and Doom are arrested and held in the new prison that SHIELD calls The Vault.

It isn't until two years later when the alien being dubbed the Silver Surfer arrives that SHIELD starts to also detain those they deem as dangerous. The Fantastic Four are only the first "supers" that SHIELD elects to take into "protective" custody, effectively and covertly removing them from the public eye under the pretense that the newly married Mr. and Mrs. Richards just want to settle down and lead normal lives. The mutant Logan, AKA Wolverine, and a late blooming mutant empath that they know very little about, Dean Winchester, soon joins them. SHIELD gets away with holding the well-known X-Man and his companion due to charges detailing multiple counts of manslaughter concerning SHIELD Agents.

Not even a year later, more trouble stirs up for SHIELD with the emergence of Iron Man and the disaster that is the Hulk; the Mr. Hide to Bruce Banner's Doctor Jekyll. They managed to detain Stark in 2010 after the disastrous events surrounding the Stark Expo, but Banner remained elusive. Then the "god," Thor, and the frozen once-thought-to-be-lost Captain America join the ranks of SHIELD's collection of high profile detainees in 2011.

And now we've finally come to the catalyst that starts it all in 2012. Within the span of a month, the "god" known as Loki was found and captured in Stuttgart, Germany, the young and rising vigilante known as Spider-Man was taken off the streets of New York City, and the Hulk was finally captured just outside of Calcutta.

Now it truly begins again, with these twelve detainees that are held aboard the newly christened Helicarrier. It begins when four of SHIELD's own agents start to have doubts about what they are doing. It begins when they decide to do something about it…

Chapter 1: A Plan In Motion

"I hate it here," Johnny Storm complained.

"You always say that, Johnny," Ben Grimm grumbled. "Every damn morning for the last five years. Why don't you go pester your sister or Reed? Leave me alone."

"Don't wanna. I'm bored."

"You keep running your mouth and I'll clobber you."

"Aaand there's the usual morning death threat. My day is complete."

"Punk. Grow up why don't you?"

"Meh. Make me."

"Johnny, stop being a brat. Morning, Ben," Susan Richards yawned as she made her way into the kitchen section of their "apartment."

This was a typical morning in the Fantastic Four's living quarters aboard the Helicarrier. Ben and Johnny argued and bickered and mocked each other more for routine-sake than because of any real dislike that they still had for each other anymore. It was a way to pass the time.

"Where's Reed? Head stuck in another project?" Ben asked Sue.

"Not this morning. He's actually trying to construct a crib," she smiled, hand stroking her still small, but rounded belly.

"Seriously?" Johnny asked, sitting up from where he was sprawled over the back of the couch. "This I gotta see. Is it that IKEA crap that SHIELD likes dumping on us?"

"Yup," Sue chuckled. "Be nice Johnny. Try to help him if you can."

"I make no promises," Johnny smirked as he headed off towards the lab section of their quarters.

"The man's a genius when it comes to designing and constructing great complicated machines, but give him normal mundane furniture to put together, he can't figure it out. He over thinks things," Ben chuckled.

"Well it's nice to know that Mr. Fantastic isn't always so fantastic." Sue smiled as she sat across from Ben at the table with a fresh cup of tea.

They sat in companionable silence for a few minutes before a sad look clouded over Sue's features.

"What's wrong, Sue?" Ben asked. "Is it the baby?"

"No, the baby is fine." Sue shook her head. "Reed and I have always talked about having one. It's just…"

"It's just that you never wanted it to be born under conditions like this," Ben said softly.

"Yeah. I hate it here," she muttered.

"You sound like your brother," he chuckled.

"The horror," she gasped.

They fell back into silence, listening to the growing commotion in the lab. Obviously Johnny was failing to help Reed with the crib. Ben wouldn't be surprised if the damn thing got broken and he had to build it himself. It'd happened before with other things. Yup. Just a typical boring day for the once great Fantastic Four.

"Come on, Cap! Show me that move again," Peter Parker insisted as they continued their sparing session.

"Ok, watch carefully now," Steve said, letting out a long breath before executing a series of jabs, slowing them down so that Peter could follow the movements better.

Peter then repeated the moves, taking a few goes before executing them flawlessly.

"That's it! You're doing great," Steve beamed.

"I'm a fast learner." Peter smiled sheepishly, rubbing the back of his head.

"Ok, I think that's enough for now," Steve sighed. "Go wash up. Breakfast should be sent up soon."

"Yum," Peter grumbled, but rolled back on his heels and headed towards their bathroom for a quick shower, a slight bounce in his step.

Steve smiled after the boy. The kid was really growing on him. They'd been sharing quarters for almost three months now, and Peter was finally starting to accept what Steve had known for a year. They were stuck here. The boy was brilliant, and Steve was strong, but there was no getting out of their swanky reinforced fake-apartment prison cell. True, they had everything they needed, could get pretty much anything they asked for (within reason of course), but this wasn't living.

After a year alone within these walls and hardly seeing anyone, Steve had begun to wish that SHIELD had left him frozen in ice. But getting Peter for a "housemate" made living more bearable. The kid was a source of nearly inexhaustible energy contained within a small lithe body. He'd nearly had a heart attack their first morning together though when he'd come out of the bathroom and found Peter literally climbing the walls out of boredom. Now he was hardly fazed when he woke from a nap to find Peter in various stages of boredom and/or relaxation on the ceiling or walls. The kid liked sitting upside-down wedged high up in corners of the room.

While Steve waited for his turn at the shower, he collected the rumpled tumble mats they'd laid out on the floor for their sparing session. He absently turned on the vintage record turntable before doing so, relaxing as the soothing music of Glen Miller's Moonlight Serenade flowed through the room.

"Nice tunes," Peter remarked as he reemerged ten minutes later from the restroom with wet hair, jeans, a black T-shirt, and a towel hanging around his neck. His steps bounced in time to the music as In the Mood's catchy beat played.

Steve smiled as the teen bobbed his head and danced absently in place, while he collected their trays from the custom-made dumbwaiter that had been installed for food delivery (the custom part being that it was made to be too small for even Peter to try to squeeze into). The food must have been sent up while Steve was straightening up their workout space. Steve was glad that Peter didn't mind his choice in music. It was nice to meet someone from this modern age of technology that had a fondness and fascination for what was considered old and classic.

Loki was bored and Thor was being annoying. They couldn't hear each other through the thick reinforced glass that separated them, so Thor had taken to tapping – well actually it was more like angrily banging – out messages against the wall between them. For now, the big oaf was being mercifully quiet. He'd nearly forgotten how insufferably obnoxious the man could be.

During his long year drifting between spaces in the void, he'd felt so alone. When he'd been captured, initially Loki'd felt strangely happy to see the surprise, relief, happiness, and concern there on his foster brother's face and the near desperation that the Asgardian expressed in his attempts to reach out to him. A younger Loki – well, maybe not a younger Loki, but the Loki from a year ago, the one who was bitter in his jealousy towards his brother and wanted to prove himself a capable ruler to who he'd thought was his father – would have mocked his brother's weak emotional displays. But as he was now, Loki just felt relieved to know that he'd been missed. Relieved to know that he still had his brother's compassion, if not his love (even if it was a result of the man's interactions with that Midgardian woman), when he clearly had none left from his father.

His trip through the void had been hellish. Though most of his year was spent adrift, he'd found himself "rescued" by an army of beings that he'd once thought only existed in legends. Beings that were the stuff of nightmares. The things he'd suffered at their hands… He would have given anything to be stuck on an idiotic quest with Thor, the self-righteous Lady Sif, and the imbecilic Warriors Three, rather than face…him.

But he had escaped! He had! …Only to wind up in another prison. In another cell. Well, at least these Midgardians were rather hospitable and, dare he say, pleasant, in comparison to the Chitauri.

Loki broke free of his wandering thoughts when Thor tap/banged out another of his messages. So much for peace.

Are you well?

Loki rolled his eyes, knocking his knuckles twice against the glass partition between their halves of the large round cell.

Yes. No.

Logan couldn't help staring down at his extended claws. He'd had them for a few years now, but they never ceased to surprise him when they came out. Before he'd been taken into SHIELD custody they had been simple bone. Now they were bones made of adamantium. His whole skeleton was. Fucking SHIELD. He wished that the Professor would just bust him out of here. But that wasn't the man's way because of the legal crap involved in this mess, and Xavier didn't know what SHIELD was doing here. What they were doing to him. To the kid.

Logan looked up, claws sheathing, when they opened the door and shoved Dean Winchester back inside their cell. Logan was on his feet instantly, steadying the kid before he could face plant. He wondered where they'd taken Dean this time. Logan didn't like it when he was away for a few days at a time. The experiments were bad enough. He didn't want to know what kind of rat maze they had the guy running through when he was taken off ship. Every time Dean came back, it seemed like another piece of him was lost. Another glimmer of light gone from his eyes. It would take longer to get the wiseass punk he'd known for nearly ten years back to even a shadow of who he used to be after sessions like this.

Dean didn't even try to shrug him off as he was manhandled over to one of their cots, and the dullness lingering in his eyes made Logan wonder how drugged up he was.

"Hey, Kid. You with me?" Logan asked once he got the younger man seated.

"Not a kid, Log'n," Dean mumbled, some light returning to his eyes. "I'm thirty-two for Christ's sake."

"Thirty-three actually, Bub," Logan huffed.

Dean squinted up at him. "Another year gone by already?"

"Yeah." Logan swallowed, eyeing the edges of what was undoubtedly an array of fading scars under Dean's shirt collar and sleeves.

"What did they do this time?" he asked.

"The usual I suppose," Dean whimpered. Actually fucking whimpered.

"You suppose?"

"I… I don't actually remember, Logan."

And Goddamn-it, the kid looked scared shitless. It was bad enough that SHIELD had been experimenting on his friend's body, giving him other mutants' powers. Now it looked like they'd finally succeeded in breaking through Dean's mental walls and were screwing with his mind. Fuckers were trying to turn his friend into a mindless drone. A weapon.

Logan knew that that was what they were doing, because they'd tried to do the same to him, but thankfully it wasn't working on him, because of his regenerative healing powers. At least, that's the gist of what he understood from Dean's long convoluted science-y babble. The kid had been very out of it when he'd tried to explain it. If it weren't for moments like that, Logan would sometimes forget that Dean was actually a smart sonuvabitch.

Kid just didn't like the attention that came with people knowing he had a brain in that thick skull, so he played up the simple-minded handsome tough guy persona that people saw at first glance. The Professor had once told Logan that Dean had one of the most complex and fascinating minds he'd ever seen. The kid had a real knack for gadgetry. Dean and McCoy had been almost scary together when they got into tinkering mode, but no one could deny the results and effectiveness of what they invented for X-Men missions and for helping mutants learn to control their abilities. And now those SHIELD bastards were messing with that brilliance.

"It's going to be ok, Kid," Logan said softly, sitting close beside his friend. "We'll get out of here soon."

"Liar," Dean whispered, but allowed Logan to manhandle him again so that they were slumped, resting against each other, side by side on the rickety cot.

Logan and Dean had never been ones for touchy feely crap (downright avoided it, in fact), but after 5 years of being held prisoner and experimented on, one sought out the only source of comfort they had, and for Logan and Dean, that was each other.

Tony Stark was bobbing his head absently to AC/DC when Bruce Banner joined him in the lab. He was not surprised to see the array of coffee rings lining the eccentric man's worktable. Tony rarely slept these days. Not since they'd managed to sneak a peek at the security feeds for the Helicarrier. Thanks to a hacking program that Tony had been working on and completed only a few days after Bruce was brought in, for ten minutes every day during the afternoon shift change, the film footage to their rooms looped and they got complete privacy. During their small sessions of privacy, Tony and Bruce had stumbled across security footage of other prisoners on their level's server.

Bruce had recognized the quartet known as the Fantastic Four. Tony had gone on and on about how he'd known that Reed and Sue Richard's gradual withdrawal from academia and the team's disappearance from the public eye had been suspicious. Tony got even more up in arms when they'd discovered that Sue was pregnant, indignant that the woman would probably have to have and raise the child in these prison walls.

Then there was the discovery that SHIELD had Captain America and Spider-Man in their custody. Bruce had been the one to figure out the identity of the teenager, having recalled reading something about the young web-slinging vigilante in the paper before he'd been apprehended and brought onto the Helicarrier. The young looking WWII vet was a surprise however. It was Tony who'd realized who he must have been, recognizing Captain Steve Rogers from the news reels his father used to have him watch as a child. It wasn't hard to figure out, seeing that S. Rogers was one of the two names listed on the camera ID.

Then a week later, Tony and Bruce had refined the hacking program and got access to footage from other levels and uncovered more prisoners. There were two men in strange clothes being held somewhere on the Helicarrier's lower level near the hanger bay. They were Thor and Loki, according to the names on the security camera IDs. But what really disturbed Bruce and the reason that Tony hardly slept anymore was the discovery of the two other prisoners held aboard the Helicarrier. In another area on the lower level near the labs, two men were being held and experimented on. One was methodically cut open and clinically studied as his skin rapidly healed itself. The other had been connected to a series of monitors and tubes and subjected to a series of tests that forced the man to react, using several different powers that were barely being controlled. Both men were in obvious agony and Bruce swore he could hear the screams from their rooms even though they still hadn't yet managed to hack into the audio feed and sync it with the security footage.

After that, Tony had poured every second of his time during their ten minute window into scouring all of the Helicarrier's security feed to see if there were any more prisoners being held aboard the Helicarrier. Thankfully there were none. Just the twelve of them. And Tony was hell bent and determined to get everyone out.

"Do you have a plan?" Bruce asked Tony the moment their ten minutes of privacy began for that day.

"The makings of one," Tony sighed, tearing his eyes away from his latest project. "JARVIS is now fully integrated into the system and I can cause a ship-wide cascade failure that will take out the security first. With that down, our doors – and by ours, I mean ours, Cap and Spidey's, and the Fantastic Four's – will open and will get my suit free. It'll come to me – that's part of it's programming. Then the lights and communications go out along with the wireless internet. Navigation's the last to go. After that, the engines fail, and because they have no way of notifying the system that they're failing, the backup power won't kick in. We have a minute to get me suited up and then a minute of free fall to make our way to the lower level to get to the others. Then the engines restart, so the whole thing doesn't crash into the ground, but by then hopefully between the eight of us, we'll be able to free the other four."

"Setting aside the very possible issue that the Other Guy might come out during this escape attempt, I have to ask. Once we're all free, how do we escape?" Bruce asked.

"You might just want to let the big guy out. Could be fun seeing SHIELD trying to deal with the Hulk on top of all the system issues I'm going to be spamming them with. But getting out is one of four problems that I haven't managed to solve yet," Tony growled. "Right now I don't have an exit strategy that gets all of us out. If it were just the two of us, I'd do what I just told you and blast a hole in the side and fly us out. But as far as I know, only the Human Torch and I can fly, so blasting out is not an option. We could steal a Quinjet, but it'll take me precious time familiarizing myself with how to pilot the damn thing."

"Ben Grimm and Johnny Storm are both astronauts and pilots. I'm sure together the three of your could figure out how to fly one," Bruce pointed out.

"Maybe," Tony grumbled. "But I doubt that either one of them has flown since they disappeared into SHIELD custody, which was what? Four? Five years ago? They'd be unfamiliar with the tech."

"Ok, piloting aside, what are the other three problems?" Bruce asked.

"Another is Pepper, Rhodey, and whoever else is out there that has a connection to our fellow prisoners. Rogers has been on ice for 70 years, so everyone he knew is either dead or will be dead soon, you've told me you have nobody, the Fantastic Four only have each other as far as I know, but Spider-Man is only a teenager. I'm sure he's got family out there somewhere. And who knows about our poor friends down in the Helicarrier's basement."

Bruce nodded. It made sense. The only reason Tony was aboard the Helicarrier was because he'd refused to turn over his Iron Man suits and designs. When SHIELD hadn't gotten what they'd wanted they went after Pepper Potts and threatened to ruin Lieutenant Colonel James Rhodes, the only two people that were close to Tony Stark.

On their first day as fellow prisoners, Tony had told Bruce about how SHIELD had threatened to ruin Lt. Col. Rhodes' career by revealing the few cover-ups the man had made for Tony during the first few months when Iron Man was new, and get their hands on the War Machine armor once the man was dishonorably discharged. Then there was the bio-weapon they'd planted in Pepper after the confusion of the Stark Expo incident. It was something that SHIELD's scientists had cooked up. If Tony had refused to turn himself and his suits in, SHIELD would have activated the nano-machines implanted inside Pepper's system that were designed to break down her body and cause all of her internal organs to fail. The presence of the nano-machines made Pepper a hostage and kept Tony aboard the Helicarrier as SHIELD's "guest" and consultant.

Bruce wondered if this was what happened to the Fantastic Four. Being rich and famous they couldn't be fully removed from the public eye. Mr. and Mrs. Richards still published scientific papers, Tony still made things for Stark Industries, and they all helped design things for SHIELD, but they did so from the bowels of the Helicarrier, not from their homes like the public thought.

"And the other two problems?"

"There's going to be security outside all prisoner doors. To get into my suit, I need them taken out, but I can't take them out without getting into the suit. And once we get out, we're fugitives. We'll need resources I'm not equipped to provide right now. We need an outside man. I could get a message to Pepper and ask her to start looking around for one, but it's going to take time."

Bruce nodded solemnly. Then they both startled when the overhead speakers suddenly crackled to life.

"I think I can help you out," a voice said.

"Agent Coulson? Shit, we're made," Tony said, closing down the monitors.

"You're not made, Stark," Coulson said. "We've been watching. We're on your side."

"Who is we?" Tony demanded.

"Agent Romanov, myself and two others, but forget about that for now. You haven't got much private time left. Don't worry about Lieutenant Colonel Rhodes and Ms. Potts. Romanov and I have already worked out a way to neutralize the threats made against them. They say hi, by the way."

Tony gaped at the ceiling.

"Figure out what you need and leave the exit plan to us. You'll be hearing from us tomorrow, gentlemen," Coulson added before the comms went down and Tony and Bruce's ten minutes were up.

That evening, Natasha Romanov sat in one of the conference rooms at Stark Industries next to Clint Barton and across from Virginia "Pepper" Potts and Lt. Col. James "Rhodey" Rhodes. Phil Coulson was standing, looking out the floor to ceiling windows that had a stunning view of the city from twenty floors up. Pepper was rubbing her arm where Coulson had had the honor of injecting her with the serum that should destroy the nano-machines in her body. Natasha knew that the two of them had become and remained friends since the Obadiah Stane incident, and that hearing what had been done to Pepper after the Stark Expo had enraged the normally calm agent. Natasha had felt guilty and that it had been her fault, even though she hadn't been the one to inject the nano-machines into the other woman. She felt as if she'd failed Coulson for letting it happen, and that she'd failed Pepper for not being there to protect her.

"Will this work?" Pepper asked.

"It should," Coulson nodded. "I think enough time has passed to find out. Clint, scan Ms. Potts."

Clint nodded and came around the table with a wand-like device in hand. Pepper stood up and allowed herself to be scanned the way the security guards check people for metal at airports.

"She's clean," Clint grinned.

Rhodes sagged in his seat with relief, and Natasha allowed her shoulders to relax.

"So what now?" Rhodes asked.

"Now we get Mr. Stark and the rest of the prisoners on the Helicarrier out. Stark has a plan to break free and we have an exit strategy," Coulson informed them.

"There's still a lot of risks, however," Natasha said grimly. "First, there's Banner. This whole plan could blow up in our faces if he lets the Hulk out. Then there's Loki. We don't know if he can be trusted."

"I'm not worried about him. I'm sure you can persuade him to be cooperative, Natasha," Coulson said. "And Banner should be stable so long as we can keep him out of the immediate action. It's Logan and Winchester that I'm worried about."

"They're the mutants that SHIELD has been experimenting on, correct?" Pepper asked. Rhodes pursed his lips in distaste.

"Yes," Natasha nodded. "They've been messing with Dean Winchester's genetic makeup and splicing other select strains of the mutant-gene into his DNA, giving him the powers of other mutants like Magneto, Mystique, and even Logan and Charles Xavier, just to name a few. The man was originally a simple Empath. Now he's a super mutant with very little control over his new abilities, as well as his original empathic ones. SHIELD keeps him docile with a cocktail of sedatives and opiates that are just a step down from what they used to knock out the Hulk."

"They've tried to do the same thing with Logan, but his regenerative genes heal his body and fight off the invasive strands of DNA trying to integrate into his genetic code like it would an infection or virus," Coulson added. "Even though Dean was given Logan's ability of rapid healing and self-regeneration, the power heals him at a slower rate and isn't as integrated into his genetic code as Logan's."

"So the reason they're able to mess with Winchester's DNA, even with the healing stuff, is because the self-healing power is an infused power unlike Logan's, who isn't affected because he was born with it. He's lived long enough that his body knows it's own make up and fights off anything it deems foreign."

"Precisely," Coulson nodded.

"So if they haven't managed to manipulate Logan's DNA, what have they been doing with him all this time?" Pepper asked.

"Mainly testing out his regenerative abilities," Natasha said.

"Yeah, and his new adamantium skeleton and claws," Clink snorted. "Wonder whose bright idea that was to fuse the guy's bones with the strongest and one of the rarest metal alloys on Earth. The guy can do some serious damage with those. I've seen the tests."

"And that's precisely the reason I worry about including those two. Logan might see this escape as a chance for revenge and go on a violent spree that might jeopardize not only our plan, but the lives of everybody aboard the Helicarrier."

"I wouldn't," Clint shrugged. "The dude was an X-Man. He saved people and taught kids for a living."

"Five years imprisoned and being experimented on can change a person, Clint," Natasha said softly. "I doubt he's the same man he was before SHIELD arrested him and Winchester. But I also doubt that he'll jeopardize our plans."

"Why?" Rhodes asked her.

"Because of Winchester," she said matter-of-factly. "I've also seen the security footage, and Logan will work with us if it means getting his friend out of SHIELD hands."

"So we're all set then," Pepper said. "The escape plan's a go, and we have made arrangements for a safe base of operations. I'll head out in an hour and collect May Parker on the way."

"And I'll be waiting for your signal," Rhodey nodded at Coulson.

"Are you sure you want to do this, Lt. Col.?" Coulson asked. "You'll be seen as a traitor and an enemy of SHIELD if you do this. You'll be going AWOL and possibly considered an enemy of the state. You will become a fugitive just like all the others. Maybe even more so."

"Considering the alternative, I would have been fired anyway and SHIELD would get their hands on the War Machine suit. Tony's fought to keep his suits out of their hands. I owe it to him to do the same. Tony's suits are all coded to him so that only he can use them, let alone open one without setting off it's self-destruct sequence. War Machine has no such fail-safes because it was given to me for use on behalf of the Department of Defense. So, yes. I'm sure I want to do this."

"Besides," Clint smirked. "If all goes according to plan, you'll be cleared of charges by the end and able to go back to working for the government. That or be part of a large team of superheroes. Either way."

"If all goes to plan," Rhodes shook his head, a small smile spreading across his face.

"I just thought of something. What about Winchester's family?" Pepper asked. "You said he had one, right?"

"We don't need to worry about them," Natasha assured her. "SHIELD won't be able to use them. John Winchester is anti-mutant and hasn't spoken to either of his sons in the last 10 years, so he's no good as leverage against Dean. As for Sam Winchester, he hasn't seen or spoken to Dean since he left to attend Stanford back in 2002. He got into law school in '05 and got his degree in '08. The guy's a high profile lawyer here in New York now, hired by Charles Xavier as a defensive lawyer for mutants at Xavier Academy. He also happens to be a strong Telekinetic and is married to a Telepath with a psych major. Sam is the golden boy in Mutant Rights circles and works directly with Doctor Hank McCoy. If anything happens to him, SHIELD risks a riot."

"Basically, Xavier has guaranteed Sam's safety by hiring him," Clint said.

"He made sure of it after Dean was arrested," Coulson agreed. "Not that it matters. Sam is going to be meeting us at the safe house. He'll have Doctor McCoy and Professor Xavier with him. They should be there already, actually, setting things up."

"Great. Now that we've made sure we've covered our bases, lets get this thing in motion," Pepper nodded. "I'll see you all at the safe house."

Aaand that's the prologue and chapter 1 of The Ultimate Avengers! :) Yay! It ended up being a lot longer than I'd intended, but that can only be a good thing for you guys, right? Next chapter will be the start of our superheroes' escape. I hope you enjoyed this. Let me know what kind of character interactions you would like to see in future chapters. Anyways, let me know what you guys think of the story so far, let me know if there are any kinds of character prompt interactions/stories you'd like to see, and if you have any questions don't be afraid to ask!

OK. Now for some clearing up about the series of events.

X-Men: First Class and Days of Future past are the only X-Men movies that happened and remain canon. In this story, because it was Raven/Mystique posing as Striker that saved Logan at the end of X-M:DoFP, Logan never joined Team X or was experimented on and given his adamantium claws, so the events of Origins of Wolverine never happened, but the mutant experiment program and Striker's Team X still occurred, just taken care of by Xavier's current-at-the-time X-Men team and SHIELD. The mentioned incident in the Prologue in 2000, refers to what happened in the first X-Men movie. Even though the timeline has changed, certain events have still occurred (like Logan finding Rogue and bringing her to Xavier Academy). They have just been resolved differently, mainly by the X-Men and SHIELD's efforts. It's mainly the X-Men timeline that has shifted (changes such as Logan's involvement with the Xavier Academy and Raven/Mystique's loyalties will be mentioned further along in the story). Most of The Amazing Spider-Man and all of the Fantastic Four and Rise of the Silver Surfer have occurred as they did in canon.

As for the Avengers characters...

For Captain America, obviously everything leading up to when he wakes up from being frozen in ice, is still canon. In this fic, when he wakes up he is already on the Helicarrier and cannot escape from his reenforced rooms.

The events in Iron Man and Iron Man 2 are canon, but afterwards SHIELD brings Tony in for a debriefing. Now because in this timeline SHIELD is detaining supers instead of recruiting them, there is no Avengers Initiative. After what happened with the Expo, Tony is asked to turn over his suits, which he refuses, and when he refuses to cooperate with SHIELD altogether, Pepper and Rhody are threatened, basically blackmailing Tony into being a political prisoner aboard the Helicarrier. He's taken out of the public eye the same way the Fantastic Four were; with a bullshit excuse that he needed to take some time away and recuperate from a health scare and what had transpired at the Expo.

Now for Thor, I'm down right borrowing (i.e. stealing) copperbadge's idea that Thor tried and found a way (by magical means) to return to Earth and Jane, but the trip left him weak and drained and made it easy for SHIELD to capture him. As for Loki, he found himself drifting through the void before winding up on Earth (I'm not revealing the exact circumstances that occurred that put him on Earth, but it's pretty much similar to what happened to him in copperbadge's Coulson's Eleven).

As for Spider-man, Peter gets arrested after the events on the Williamsburg Bridge, but before the confrontation in the sewers and Doctor Connors makes his bio-chemical cloud compound. The reason I picked this particular point in the movie's canon is because I think that Connors got slightly desperate and hurried his plans after finding out that Peter was Spider-Man after he found Peter's camera. With Peter/Spider-Man out of the picture, Connors can take his time and does so in this fic, waiting months to perfect his chemical formula and revenge against Oscorp.

OK, I think that's enough about the story. Now for the characters and pairings.

Right now I'm only working with the following pairings/couples: Pepper Potts/Tony Stark, Natasha Romanov/Clint Barton, Reed Richards/Sue Storm, Peter Parker/Gwen Stacy, Jean Gray/ Scott Summers, Jessica Moore/Sam Winchester, and Dean Winchester/Raven|Mystique. If you have any ideas for other pairings please let me know. I don't mind slash pairings, but I would like to try to keep the Marvel canon pairings for those who don't really care for that sort of thing.

If you have any questions about the characters or the story, please feel free to leave a comment in a review or PM me. Look forward to chapter 2!