AN: Finally posting this after working on it since July 2012. Hope people like it!

Disclaimer: I do not own the Avengers or Transformers.

Part One: Biohazard

Chapter One: War

By ObsydianDreamer

[Steve]

One Month Before

It was a quiet day like any other in New York City. For the Avengers, this meant relaxing in the recreation room of the newly completed Avengers Tower. Tony, who had designed the building himself, had spared no expense.

The huge building had individual floors for all members of the Avengers and even one for Coulson. The tower also had everything they would need, with gyms, communications rooms and science labs. It had a few things that they probably didn't need as well; including a multi-floor laser tag arena and a pool which Tony had adamantly insisted on keeping.

So there they all were, in the recreation room of the great Avengers Tower, each peacefully doing their own thing. Clint and Natasha were sitting at the table, sifting through piles of profiles, looking for new SHIELD recruits. Natasha looked utterly bored, and Clint had given up completely, leaning back in his chair and playing some kind of game on one of the small wireless devices.

Thor, meanwhile, was rummaging through the adjacent kitchen, searching for a snack. His appetite was the biggest of them all, and he easily and regularly ate everything they had. Thus, restocking the kitchen was often a priority.

Tony and Bruce were discussing something to do with science. What exactly, Steve wasn't sure about. He picked up random parts of their conversation; "Gamma spectroscopy" this, and "Quantum string theory" that. Confused, Steve turned his attention back to the book he was half-heartedly reading. Despite having missed out on decades while frozen in the ice, Steve was in no rush to catch up; instead, he thought, he'd do it when he was ready. Putting the book aside, Steve settled down on a couch situated near one of the massive glass windows and gazed out at the city below. After a minute he closed his eyes, only feeling the warm rays of the sun through the window glass.

It was comforting.

How long he stayed like that he wasn't sure, but he was shaken from his trance when a very worried looking Maria Hill barged into the room. She was flustered, her cheeks tinged red and her breath short.

"You're all needed in the communications room." She said urgently. "There's a situation."

Without another word they all got up and followed her out of the room, and to one of the elevators at the end of the hall.

"What's happened?" Steve asked. He'd never seen the agent so tense before; whatever had happened, it couldn't be good.

"SWORD just received a message from deep space. It's from a hostile alien race. The address is getting transmitted to the communications room as we speak." She replied, pushing the button on the elevator, closing the doors.

"Wait a moment. What's SWORD?" Bruce asked, curiously.

"Sentient World Observation and Response Department. It's a subsection of SHIELD that deals with aliens. Established after the Chitauri invasion." Maria replied. The elevator door slid open and Maria walked ahead, scanning her ID to open the doors to the communications room.

Until that moment, Steve hadn't been in the room yet. It was a huge hall, filled with technology he didn't fully understand yet. It had rows and rows of the "computers" that Tony had once tried to teach him to use, but to limited success. On the left side wall, were a series of large monitor screens. At that moment, three of the screens were in action; one was showing Nick Fury, who was back at the main SHIELD base, one that said NEST headquarters, but wasn't currently operational, and the other showed the broadcasted message of the alien.

Steve had never seen anything like it before.

The alien looked like it was made of metal and machines, all twisting, locking and joining together to form a face. In some ways it resembled Tony's Iron Man suit, except it was much more rusted and damaged. It had two ruby-red eyes that glowed, and half of its face was blown off.

"What is that?" Steve not-so-quietly asked Maria Hill. Surprisingly, it was Thor who answered.

"A Cybertronian. They were a once-proud race of metal men. They're not of the Nine Realms, but we used to be on good terms with them until their civil war. There are few of them left now." Thor stated, and pointed to the Cybertronian on the screen before continuing. "His name is Megatron, and he started the civil war when his brother was named their leader instead of him."

Steve expected Thor to continue with the story, but instead he stopped talking and seemed to turn rather melancholy. Realising that a very similar thing happened between Thor and Loki, Steve decided not to press the issue any further, turning his attention to the screen where Nick Fury was about to speak.

"Let's skip to the point, since we already know who and what you are. What do you want this time?" Fury said, his voice clear through the speakers.

"It's simple." The Cybertronian said. The voice sounded somehow familiar to Steve, but he couldn't be sure where from; it unsettled him. "Hand over control of earth's resources, or we begin our attack."

"No." Nick Fury replied, his voice was strong and clear, and not worried the slightest bit. "We've defeated you before. Mission City. Egypt. We even have a Special Forces division dedicated to stopping you, in case you haven't noticed, that even has members of your own species determined to defeat you."

"The Autobots are of little concern." The Cybertronian replied. "They can be dealt with easily. This is your last chance, insects. Surrender, or else."

"I'd seriously reconsider your plan, Mega-man, or whatever Thor said your name was." Tony cut in. "Not only is half your race against you, but you've also got the military, and most importantly, us, against you. The Chitauri tried, they failed, what honestly makes you think you've got a chance?"

"Insolent little insect!" the Cybertronian snarled. "You claim that your planets champions will defend it, but you inferior flesh creatures are not prepared for the warfare we bring!"

Everyone in the room suddenly became very nervous. What kind of warfare were they not ready for? Before Tony could say anything else, Natasha pulled him back and told him, very explicitly, to keep quiet.

"If you attack us, we will fight." Nick Fury said angrily. "We are prepared and we will respond aggressively to any hostiles!"

The Cybertronian chuckled.

"I was hoping you'd say that." The cybertronian replied. "So be it. Prepare for warfare unlike anything you've faced before." The transmission from the aliens cut off very suddenly, leaving the entire room in silence.

"Coulson, Hill, get the satellite feed to the NEST headquarters in Chicago up and running and relay the transmission." Nick Fury ordered, before turning towards the team. "Also, you guys might wanna suit up."

AN: Hey guys! Thanks for reading! Just a few things:

Please review. If you liked it, review and tell me what you liked. If you hated it, review and tell me why. If you have constructive criticisms, please review, so my writing can get better.

Also, I won't be filing this under crossovers just yet. The Cybertronians don't appear again for a while; they'll only be mentioned.

Thanks to my beta readers Baylee Shadow and Tanya Meridia.