A/N: So I'm not sure if this has been done yet or not, but here you go: a Big Hero 6 and Captain America cross over of sorts.
This is meant to be a real-world AU, so here's a list of actors/actresses to reference in case you need some help seeing cartoon characters as real in your mind's eye. I'm not including the actors from Captain America because you already know who they look like. Including Pierce and Whitehall just in case you aren't altogether familiar with them though.
This first chapter is a prologue and happens at the beginning of Big Hero 6; the rest of the chapters happen sometime after Callaghan's arrest as well as the end of Captain America: The Winter Soldier.
Anywho. Character list:
Reed Diamond as Doctor Daniel Whitehall (original actor)
Robert Redford as Alexander Pierce (original actor)
Ryan Potter as Hiro Hamada (original actor)
B.J. Britt as Wasabi
Daniel Henney as Tadashi Hamada/Desert Soldier (original actor)
TJ Miller as Fred (original actor)
Jadyn Wong as Go Go Tomago
Robert Patrick as Callaghan
Camille Guaty as Eliza/Callaghan's assistant
Katharine McPhee as Honey Lemon (or another actress if anyone can think of it; I had a hard time thinking of an actress similar to her appearance.)

"I've gotta grab one more think, Hiro. Wait out here, I'll be back in a sec," Tadashi instructed his brother. Still flying high from his acceptance to SFIT, Hiro hardly even heard him. Something vaguely told him that he shouldn't leave his brother, not tonight, but an even stronger impulse drove him towards the room. Tadashi slipped into said room, where Professor Callaghan was waiting. Two other men, a wiry guy with gray hair and glasses reminiscent of the '40s and a more squarely-built man, whose flamboyant manner was practically unbearable, stood off to the side. Doctor Whitehall and Alexander Pierce. Tadashi purposefully avoided the men's gazes, touching his forehead a moment before throwing Hiro's neurotransmitter headband towards Callaghan.
"Good job," Callaghan nodded his approval, and Tadashi stood silently, awaiting his next orders. "You may be excused."
"Happy to oblige," Tadashi said automatically. He turned on his heel to leave, but Pierce set a hand on his shoulder, stopping him. Tadashi instinctively yanked away and stared at him with mistrust and fear. Pierce basked in it.
"One more thing, Desert Soldier." Tadashi swallowed at the mention of his new "handle"; the thing that HYDRA called him after his brainwashing. "Hail HYDRA."
Tadashi stood erect and held both arms straight out in front of him. "Hail HYDRA!"
"Good," Whitehall said, nodding. Tadashi turned and left the room in a semi-confused state.

His head felt fuzzy, but he remembered he needed to catch up with his brother. "Hey, bro. Let's head to the cafe."
"Geez, you took forever!" Hiro exclaimed.
"Not really," Tadashi shoved him teasingly. "You're just excited."

Callaghan nodded to the two other men. Pierce slipped out, Callaghan left the room in search of the microbots. Doctor Whitehall rubbed his hands together and started searching the cupboards for the chemical mixtures he needed. It would start as a slow flame; the expo hall would do the rest. Callaghan met up with his assistant, Eliza; a fellow HYDRA agent. "You need to get out, but whatever you do, don't forget his trigger words," he said in passing.
"Yes sir," she nodded curtly, picking up her clipboard.
Callaghan took a deep breath as he found the microbots, settling the neurotransmitter band over his wrinkled brow. Five, four...he focused on the microbots...make me a shelter. Make me a shelter...three, two...there we go. And...one.
Whitehall rounded the corner just before the blast shocked the event hall. Screams flooded the building, and hundreds of people immediately started pushing towards the emergency exit. The flame soon cut their pathway off, so the herd of crazed humans jostled for the main entrance, which was slowly licking up into flames, too. Whitehall pushed through the crowd, making it out safely and calling out, "I'm a doctor! I can help you. I'm a doctor!" Plenty of individuals pressed towards him, and his presence was engulfed, invisible in the crowd. Perfect.

Eliza tore through the crowd of people, her eyes darting as she searched for the Desert Soldier. Named for his unwillingness to desert his family (but pronounced desert as in the Sahara desert), this next step was crucial. Desert Soldier needed to forget all of this - but still remain somehow intact. As with the Winter Soldier Project, destruction in order to preserve wasn't new to Eliza or anyone at HYDRA, really. Her eyes locked onto Tadashi, and she ran forward, tripping and choking.
"Professor Callaghan's still in there!" she cried. His trigger sentence. No matter what happened, he'd go in there. Oh, of course it would be discreet and nobody would guess foul play - and he'd die the silly boy who tried to help, not the brainwashed man that had no other choice. They'd been so careful with his brainwashing, making sure they left no marks - and picking him up during the week-long expo a month ago, when he'd told Callaghan of Hiro's invention; brainwashing him and having him back to normal by the end of the week had been tedious, but it had been done. She almost felt a twinge of pain at this thought. They'd gone to such lengths to ensure that he held no injuries after the brainwashing, and now...

The second explosion threw his little brother back, and he was left shrieking his brother's name.

Tadashi crouched in the far corner of the hall, covering his head. Something had severed his right arm and his ears rung, but he was otherwise unharmed. He'd sensed the explosion moments before it happened, and had thrown himself as far away from it as he could.
"Callaghan!" he now screamed, his throat tearing and constricting as he gulped in the smoke. His trigger code - it meant he had to find and protect Callaghan at all costs! If not, he'd-he'd...who knew what Doctor Whitehall and Alexander Pierce would do to him! He couldn't remember, but he knew it hurt. He pushed through debris; didn't even notice when his left leg caught fire. He saw the massive mound of microbots and gasped in relief. The microbots fell down to reveal the professor, but then they reformed and grabbed him up in a large fist, squeezing him until he was enveloped in a black abyss.