Disclaimer: I do not own any part of BtVS, Prototype or any of the mentioned characters in this story. They belong to Joss Whedon and Dark Horse comics, Activision Publishing Inc and DC comics was involved because their banner is seen throughout the game and they're publishing the comic book version of the game.
The moment Xander's head hit the ground he fell into a deep sleep.
"Hello Xander," said a deep voice.
Xander turned his head and saw himself wearing a grey hoody, a black leather jacket and grey jeans.
"Who are you?"
"Well technically I'm your subconscious and thanks to tonight's events we've gone through some changes."
"What are you talking about? I just dressed up as a soldier version of myself and…" he was still a little stunned when he looked back on his memories.
"But, it wasn't really soldier-version you behind the wheel was it?"
"No, it wasn't. Who was that guy?"
[Flashback]
Alex Mercer stared around in shock. Never had something like this ever happened. He had consumed over two hundred people and creatures. Never had this happened. One second he consumed a lieutenant Harris to use his form as a disguise and the next moment he was standing in a suburban area that definitely wasn't anywhere near New York. He quickly jumped onto the roof of a nearby house to get a better view while changing back to his original form. Through infected-vision he immediately saw that none of these beings were infected by the Blacklight virus. But, not all of them were human. Even with all his memories, the only decision that he could make was that he wouldn't let the innocents get hurt. He quickly jumped into the air and started to glide over the town.
A serpent-like creature was chasing a little girl. He quickly crashed into the creature and while it was on it's side he cut off it's head with his clawed hand. He was splashed with acidic blood that quickly ate at his exposed tissue. He needed to consume someone quickly to heal even with his body starting to neutralize the blood. Seeing a wacko throwing lightning at what clearly looked like a superhero. He leaps for him and consumed him immediately. After he was fully restored he continued to patrol the town.
He saw a girl being attacked by a pirate of all things. He quickly ran towards the pirate and body checked him so hard that he hit the wall behind him and slumped into unconsciousness. But Alex felt rather good for doing it. The girl's friends quickly arrived and started to comfort the girl. It appeared that they were being followed by a group of what they called 'demons'. Getting tired of this night he simply jumped into their midst planning to kill them all in one go with a devastator Tendril attack.
At the last second the redhead in the leather screamed "Don't harm the small ones they're just children."
"Fine" He quickly knocked out the small ones and cut down the larger ones. The last one was a bleached blonde who tried to run away screaming, "I should have stayed in tonight." after only a single warehouse Alex caught up to him climbing down a sewer drain. But before he could give chase a wave of dizziness overtook him and he retook the guise of Alexander Harris.
[End flashback]
"His name was Alex Mercer. He was basically a virus in human form," the mental construct said.
"How is that even possible and how could he be the one in control of soldier-version me's body"
The construct's face took on a sneer before answering. "In his reality the Military tested biological weaponry on a small town filled with volunteers who thought that they were participating in a psychological experiment. Only two people survived. Elizabeth Green and her newborn baby son."
"Let me guess. The military captured them so they could figure out how they did that."
"Yeah, they even started a shadow company called GENTEK to oversee the research and sell any medical applications to the public. Alex worked for them but when he found out he tried to go underground and took a sample of the Blacklight virus with him. When they found him at the train station he released the virus."
"Why would he do that? That's crazy," Xander said incredulously.
"He wanted to take as many with him as he could," his subconscious answered. "Some hours afterwards his corpse woke up in the morgue. The virus had consumed his body and had become sentient. Because it had Alex's memories from before he found out about GENTEK it thought it was Alex and that somebody had changed him."
"What do you mean changed?"
"Shortly after he woke up he got shot by the military and survived without any visible damage. Later he discovered many other abilities and used these to discover his past and save the city of New York from total annihilation. One of these abilities was the ability to gain a person's memories, skills and appearance by consuming them."
"That's disgusting. Are you telling me that this guy ate people for the fun of it?"
"No, he primarily consumed people from the evil Blackwatch operations and marines when he was severely hurt in a fight or scientists who were involved in the project. It was after he saved New York that he was still doing cleanup that he consumed the Alexander Harris of that reality so he could use his appearance as a disguise"
"Alright, so what did you mean when you said 'We've gone through some changes'"
"Well except for two differences we're Alex Mercer. You're the dominant personality and you've got a direct interface to your subconscious. Me"
"So you're telling me I'm a walking human shaped virus with a split personality disorder." Turning away from the embodiment of his subconscious Xander screamed. "It's always me I'm always the universe's butmonkey bad stuff always happens to me, always."
"Look I'm your subconscious and by a quirk of fate and magic we can communicate directly so I don't have to be all cryptic with dreams to get my messages through."
"Oh, what can you do?" Xander asked sarcastically.
"Thanks to our new genetic memory, I can go through the complete memories of over two hundred people. I can also give you specific data about the condition of our body and warn you if we come into contact witch any new substances."
"Ok, that's impressive. But, how do I know you're not evil or going to take over this body?" Dread was filling his voice.
"We both need each other to function. Without me you would lose control over most of our body and without you we'd be stuck in a catatonic state for the rest of eternity"
"Whoa, wait. What do you mean by eternity?"
"We're a walking virus with complete control of our cellular structure. Alex withstood a nuke at close range. Unless they go through some extreme measures they won't be able to kill us."