Author: So, I've been playing Prototype 2 a lot lately. A lot (since I don't currently have 1). Because of this I've felt the want to make a fanfic based on it. This is my take on it and my design, set after Prototype 2 with a different ending that leaves Mercer alive and the pair to team up for awhile (unless things work out). I'd really love to hear your opinion on it, readers, so review. n_n I'd be much appreciated. Feedback is good. Do you like the idea I'm working on or should I change something?

Disclaimer: No, I do not own Prototype, Alex, Dana, Heller, Rooks, or anything in the game. I just own the characters I designed.

[Chapter 1] - Alternate Start

Everything that day had actually gone far different than predicted. He had learned a far worse truth than he had anticipated. Assuming the death of his family was because of that viral punk James Heller had originally set out to do what he could, later swinging toward bringing down Alex Mercer when he discovered that he was responsible for the second outbreak. Who would have predicted that instead of killing Mercer he would learn a more dangerous truth.. a truth that would force the pair to join up. Alex was the least of his worries.

Putting the pieces together had been a very difficult task, but as it was being set it wasn't the picture he had imagined. He hoped and prayed that once Alex was out of the way things would look up, that he would save the city from the virus, from the monsters.. but while targeting Mercer he overlooked a very important fact. Something wasn't right.

Gentek was far too quiet, though his encounters with Koenig and Sabrina, who both turned out to be from Mercer's Evolved army, proved a different light. They had been defeated far too easily. Sabrina had been hiding something from Mercer and him, but it was too late. Alex had killed her.

The thing that had stopped Heller from getting rid of Mercer was a very important thing.. a detail he had overlooked. While searching through the memories of someone he had consumed he had stumbled upon a very prominent word. Gemini. Assuming it had been something minor, like perhaps in relation to the Redlight and Blacklight virus', he had not realized that Gemini meant something else.

When he had been about to fight Mercer a memory had appeared in his mind, demanding his attention. Before he realized what was going on his mind became warped with this memory and he blinked to see Mercer standing over him, pinning him to the roof the pair stood on.

As if sensing something was amiss Mercer had got off him, backing away at the blank stare that Heller had been giving him. Hands on his hips, the black haired infected waited patiently for the older man to come back to reality.

The memory was of a cell.. that contained two little children, a boy and a girl, and above the door was a capital word that made his blood chill. GEMINI.

A conversation came with it, a shadowed male face grinning as he spoke. "This is completely brilliant."

A female voice spoke up. "What is, sir?"

"The fact that we framed Mercer so he would become a distraction for Heller." The male chuckle as the memory then showed him walking down a hall with his hands folded behind his back. He paused to turn and look at the female speaker. "It was a genius strategy. Who would have thought that while they go toe to toe, bent on killing the other, a more dangerous creation lurks in waiting."

"Are you.. referring to the twins?" The female asked hesitantly, as if trying to understand.

The shadowed man nodded. "Of course. When Heller kills Mercer they will kill him." The memory changed angle and it showed him sitting in a chair. "All is going as we hope."

Another memory surfaced. It revealed a tall man in a cell, his form shadowed with a deep grey blanket, but Heller could see chains trailing out from underneath, locked to the floor a few inches away.

"How much longer before Sagittarius is done?" A sharp male voice whispered.

Another voice answered, "A week? A month? A year? We don't know, sir. He's not complete at the moment."

"Continue to advance him. I want him finished before we're forced to send in another bomb to level the city."

The man nodded, the voices just out the celled door of Sagittarius' room. He stirred, lifting his head as the cover shifted down. His head was concealed in darkness, but his eyes slowly opened to reveal amber orbs that swirled with contained emotion. His lips shifted, now visible, and he slowly began to smile.

"We have a lot of work to do before he's ready for what you're asking, sir. Right now he wouldn't stand a chance."

"Make him stand a chance, doctor."

Finally shaking his head, Heller had stood and stared at Mercer with a shocked expression on his face.

"What?" Alex had demanded of the expression, obviously confused about what had caused the change in emotion.

Heller's deep voice had been strained with the fading memory and his surprise so it came out in a whisper. "It's a lie."

Alex had arched a brow beneath his hood, shifting his weight. "What?" He repeated irritably.

Heller looked off into the distance, searching for the Gentek building. "It was a setup. This.. is a fucking setup. We shouldn't be fighting." He then turned back to face the fellow infected, his eyes wide. "Gentek set us up, those mother fuckers."

"You're not making any sense, Heller. Explain." Mercer growled, frustration heavy in his words. He wanted nothing more than to rip Heller apart because of his intervening. He had set his goal back because of the killing spree of his Evolved.

Heller had thrown up his right hand, using it as a gesture as if to give life to his next words. "A memory just revealed a trick. Gentek was using you to distract me from learning about their side projects."

"Side projects? You do understand that I had people in Gentek- the very same people you killed -that could deny there being any side projects." Mercer replied with a scoff.

"That's because they were authorized through outside means. Raymond McMullen must have had them under wrap when he first created Gentek. The projects wouldn't have started until after the first outbreak. It makes fuckin' sense now." Heller stated, his tone proud, as if he had just discovered the meaning of the universe and it was the greatest thing to him. "They were under a different branch to keep them hidden."

"An interesting theory, but you have no evidence that proves you're telling the truth." Alex responded automatically with his more skeptical side, eyes narrowing beneath his hooded shadows.

"The memory was from Roy Stanson, a doctor who worked with fuckin' Gentek, but under a medical association.." The pieces were clicking into place quicker as he spoke. "He worked with two main projects: Gemini and Sagittarius, both zodiac references. The Twins and the Archer."

He closed his eyes for a moment, letting the knowledge of Roy fill his mind as he worked through the information. His eyes opened to stare at Mercer.

"The Twins.. If I kill you the Twins will kill me-"

Mercer lifted his hands, waving them up and down slowly a few times in a 'slow down' gesture. "You're losing me. Twins?"

Heller took a deep breath and dove into what he was discovering. "Infected twin children that were created to kill infected. To kill you, originally, but when I became infected they decided to use me to kill you. Realizing that they couldn't control me the Twins were going to get rid of me once you were out of the picture-"

"So you're suggesting.. what?" Mercer interrupted him, shifting his weight to the left foot. "That this doctor Stanson helped create something that could kill us both.. these Twins?" He smirked, the expression visible and clear. "I knew you were bat shit crazy, Heller, but you've blown it out of proportion. Where is your proof?"

Heller smiled now. "We hunt down those who worked with Stanson, like Reed Archer and Stephen Victor."

Mercer's eyes narrowed more. "Wait. Reed Archer? I know that name. He's the cousin of Karen Archer."

Heller nodded his head before taking a step back. "As much as I want to pound your face into the ground I believe that we have a much larger threat to face.."

"Are you implying we team up? What makes you think I won't kill you for the trouble you've caused?" Mercer asked defiantly.

"Like hell you could kill me. Besides you'll need me to put down Gentek fully." Heller said with a smirk on his dark-skinned face.

"Alright, what do you suggest we do?" Mercer had questioned.

Heller's smirk widened and he began to chuckle. "What we do best.. destroy."

That was how one thing had ended and another grew to take its place. Two people with a common interest.. two extremely abnormal men pit together in a duet of power, to finish what was started before their infection.

Author's Note: Leave a review, tell me what you think. :3 Thanks. Adios for now.