Okay then here we go. First off I own nothing except for a few Original Characters, anything else that was not in or hinted at in either Prototype game is based off other games or movies.

Editing done by He Who Sees, trust me if he hadn't helped this wouldn't make any sense.

If anyone has any questions I will at least try to answer them in notes at the beginning or ending of each chapter. Also a quick note here that will be appearing more then once over the course of the story.

Note: Threat Levels. New entries will be added as the story progresses. If anyone thinks I misplaced something by it's Threat Level feel free and welcome to say so and offer reasons and where you think it should go. Threat Level is based on multiple factors such as speed, strength, durability, destructive potential, etc. Example: The Threat Level of Walkers is 1 because they are slow, weak, fragile, and are not a credible threat to anything above Threat Level 2 and only a minimal threat to humans who know how to defend themselves. The Goliath is Level 5 because despite it's limited speed it is extremely durable and highly destructive while the Evolved fall into this category as a result of their mobility and versatility as opposed to sheer destructive force.

Level 1: Walker/s. Level 2: Armed Humans. Level 3: Brawlers, APCs, Orion Super Soldiers, Single Gunships. Level 4: Tanks, Juggernauts, Strike Teams, Hydras. Level 5: Evolved, Goliaths.

Note: Alex Mercer, Codename: ZUES. Possibly responsible for the Second Outbreak. Threat Level: ?

Chapter 1: Infected

New York / Manhattan Island / The Red Zone / Marine Patrol Route: Three-Four.

James Heller sat staring into space, the conversation between his squad mates filtering through the scattered thoughts and emotions that had plagued him since he was told of his wife and daughter's deaths. He didn't care what the other Marines were saying. It didn't concern him what they thought of Blackwatch or the Infected. The only thing that concerned him at that moment was whether or not he would find the end he'd been searching for since coming to the Red Zone. The next thing James knew, he and his squad were tumbling about inside the APC as the vehicle itself was hurled through the air by an impact they hadn't had a chance of avoiding. The next thing he was aware of was the hard concrete against his face.

Climbing to his feet, James radioed "Red Crown", Blackwatch's command center,that many Marines half jokingly said was run by a robot. Before he could report his squad's status, a crash followed by a deafening roar drew his attention to an area obscured by smoke and rubble. Through the smoke came Alex Mercer, landing heavily on the street and scattering debris around the wreckage of the APC and other vehicles.

"Alex Mercer..." James trailed off, ignoring the response his words prompted from the man who had responded to his call.

"Alex Mer-!? Oh Shit! Red Crown, we've got Alex Mercer in RZ Grid three-four! Repeat Alex Mercer is in RZ Grid three-four! We are awaiting your command!"

"Ninja Three-Three, this is Red Crown. We are sending reinforcements to your location. Do not pursue Mercer. Repeat. Do not pursue Mercer."

Heller shut off the radio, having no intention of obeying the orders. While this had been occurring, Mercer had been examining the bodies of the now deceased squad as if he were looking for something. The moment James drew his knife, intending to sneak up on the psychopath and slit his throat, Mercer turned as if he had heard the small sound.

James froze for a second when Mercer's cold blue eyes turned on him, but just as quickly shook off his uncertainty and rushed forward. Changing his grip on the knife halfway between where he had stood and where Mercer still stood unmoving with a curious expression on his normally stoic face, James leaped forward to cover the last few feet and plunged his knife into the Mercers chest at an angle aimed for his heart; assuming of course, that he had one.

As the brief rush that had come when he thought he had killed the murderer of his family subsided, James stared in confusion at the unchanged expression on the man's face. Mercer raised an eyebrow before speaking. "Good to see you Sergeant Heller. I was starting to worry someone else may have gotten to you first or that you had managed to die out here..." He paused as he glanced around, ignoring the knife in his chest. "…unfortunate that the rest of your squad seems to have died."

Just as he recovered from his shock, James was hurled backwards, losing his grip on the knife and landing painfully on the cracked street. He looked up just in time to see its handle sink into Mercer's chest and disappear.

"If you'd meet me upstairs, we have a few things to discuss."

With that, Mercer turned and shot into the air, landing on the roof of a nearby building and vanishing.

"Bastard!" James muttered under his breath before glancing around to find a weapon. After retrieving an assault rifle and a few grenades from the wreckage and corpses of his dead squad, Heller kicked open the nearest door and entered the building.

A straight hallway with a few scattered bits of debris was all James could see from the door until one of the zombie-like infected shambled out of a room near the other end of the building. The moment the thing noticed him, it rushed towards him, growling and grunting as it did so.

Three rapid shots rang out and the infected fell to the ground and another shot to it's head made sure it would stay there. James continued through the building as calmly as he could as the infected weren't his target; they were just an obstacle. No reason to bother wasting his anger, or his bullets, on them.

Though he doubted it would be functioning, James checked the elevator first just in case and wasn't surprised to find it wrecked.

"Mercer...go ahead. Hide. Break the elevator. I'm still coming for you." James muttered as he turned and headed for the nearest flight of stairs. Had he been thinking straight, it would have been obvious that Mercer wasn't afraid of him and had no need to place any obstacles in his path. But of course, one shouldn't expect a man like James Heller to be rational given the situation at the time.

While the first floor of the building had miraculously only been occupied by a single infected, the stairway and successive floors were far more populated. When possible, James simply knocked infected out of some nearby windows and down the stairs, knocking them through holes in the floor a few times.

It was simple enough to deal with the mindless creatures when they were only in front of him, but upon reaching the third floor, or rather, being halfway between the second and third floors, James found himself being attacked from both directions.

Kicking those who were stumbling up the stairs and flipping those above him to hurl them down on their fellow infected, James progressed to the third floor. To his great irritation though, he quickly discovered that the stairs above had collapsed, blocking his path to the fourth floor and leaving him surrounded on the third floor landing.

Bull rushing his way through the infected, James rolled into the hallway of the third floor and rose to his feet, dropping a pin to the ground and tossing one of two grenades back onto the crowded landing before ducking into an alcove.

James dashed for the opposite stairwell as soon as the grenade had detonated only to find his path again barred by shambling corpses. Three round bursts of fire put one after another on the floor as the man, who could have passed for a mental patient escapee from a Veteran's hospital, made his way forward.

An infected leaped onto James' back just as he reached the landing and found that he could indeed proceed from there to the fourth floor. Heller jerked to his left and elbowed the hitchhiker in the side, causing it to stumble and lose it's grip on him before he repeated the motion in reverse by slamming his right elbow into the zombie and following through the spin until he was able to bring his rifle up and put the last two rounds from the clip into the zombie's face.

After fighting his way up the next two floors and reaching the sixth, James found that the staircases on both sides of the building were impassable and the floor itself was densely crowded by the disfigured bodies of infected. It didn't take him long to make the decision to use the fire escape.

Thwarted once again when he found that the metal emergency stairs were only stable enough to take him to the seventh floor, he re-entered the building, cleared the room he found himself in, ejected the now empty clip from the assault rifle, and reloaded; very much aware that he only had one more clip after the one he just put in.

James heard a roar and felt the building shake as he cautiously made his way toward the stairs which he hoped would finally lead him to the roof to confront Mercer. The source of the roar made itself known seconds later as a large brutish creature crashed through a closed door between him and the stairs.

The monster turned glowing yellow eyes on the human and roared once again before charging, clawed fingers leaving deep gashes in the floor. The animal, which he couldn't help but see as a freakish cross between a dog and a gorilla, bared its teeth as it sped towards James.

Heller managed to put nine bullets into the creatures head, which only seemed to anger it further, before diving out of it's path into a room to his left. The Brawler crashed into a wall as it attempted to change direction before stopping completely and smashing it's way into the room Heller had escaped into moments earlier.

James hadn't opted to remain, however, and was hiding around a corner in the next room connected to the one the Brawler had just unceremoniously entered. The monstrous beast growled and sniffed loudly before roaring and leaping forward. The jump carried it through the wall and into the room,only a foot to the right of and slightly above the head of the waiting man, who shouted a single word as he dived away.

Heller was crouched and faced the Brawler as it turned to face him. Six more bullets punched into the beast's head, eliciting an enraged roar, but seemingly not harming it at all. Realizing that his weapon was doing little more than this, James decided to expend his last grenade on the beast; a grenade which unintentionally found it's way into the Brawler's roaring mouth.

"SHIT!" James rolled behind an overturned sofa just as the Brawler's teeth and most of it's skull were blown clear across the room. The teeth embedding themselves in the walls, some clearly having passed through the space previously occupied by Heller.

James was overjoyed to find that the last three floors were almost devoid of infected, simply clubbing to death those that were present with a metal bat he'd found lying under some debris after his encounter with the Brawler. James dropped the bat on the landing just before going out to face Mercer again, remembering how little the knife had troubled the man and doubting the meager (relatively speaking) blunt force of a baseball bat would do him any good.

James smashed the door off it's already damaged hinges and stepped out onto the roof. There stood Alex Mercer at the edge of the building, holding another of the creatures Heller had just killed in the air by it's throat. The freakish animal was quite clearly dead; a fact reinforced when Mercer casually tossed the corpse off the roof to crash thunderously to the pavement below.

"Glad you could join me James. Sorry about the other Brawler by the way, though I have to admit, you seem to have handled it well." Mercer said with a wry grin.

Heller's rather inappropriate response was to snarl and raise his gun before emptying his current clip into Mercer's chest before reloading the weapon with his last and promptly repeating the action. He was enraged to see the man remain standing and simply quirk an eyebrow at him.

Alex held out his right hand, fingers open and palm facing the ground, and a steady stream of metal shards fell to the rooftop and scattered around his feet while the holes in his torso melted away. "That won't work James."

"Bastard! Just die!" Heller shouted. The soldier shifted his grip on the gun so that he was holding the barrel and charged toward the terrorist.

Before the gun could be used as a club, Mercer's left arm lashed out and snatched the weapon from James. "It was amusing the first time Heller, but now you're starting to annoy me." Alex said as he twisted the gun in half before tossing both pieces away.

An indecipherable growl escaped from Heller as he threw a punch at the man responsible for his family's deaths. The first punch sailed through empty air as Alex leaned to his right. The second punch likewise met no resistance as Mercer again shifted his position causing James to stumble. This continued through a series of increasingly wild and reckless attacks by the Sergeant until Mercer decided he was tired of being nice to the human.

A sickening crack briefly lead James to believe he had accomplished at least something against the monster he was fighting. That line of thought cut off abruptly when a spike of pain alerted him to the fact that his hand was broken.

Alex sighed impatiently while the fool who had broke his hand on his face screamed. He wasn't sure if it was impressive or depressing that the screams seemed more out of anger than as a reaction to the pain of shattered bones. Mercer allowed a low growl to escape him when he heard the distinct sound of an approaching strike team.

"You should have just let me explain; now we have to do this the hard way." Alex growled out as he quickly moved behind the injured man, placing his right hand at the base of his skull. "Sorry in advance if this kills you. I haven't had the chance to test it on a human yet."

The next few seconds for James Heller consisted first of a strange numb feeling spreading through his body, starting at the base of his skull, followed by an unpleasant tingling sensation, like his skin and muscles were moving on their own. A scant few seconds after he had almost lost all feeling, James was viciously reintroduced to pain, his broken hand forgotten in the shadow of the agony he was now feeling. It was as if he had been set alight and someone was trying to rip him apart from every possible direction at once while his own body made an incredible effort of its own to implode on the spot.

For what seemed to have been hours to James, the pain continued before he suddenly felt nothing. It was instantaneous; the pain was there and then it wasn't. He could hear the sound of gunfire in the distance accompanied by roars and screams of terror followed by a deafening silence. He knew Mercer was there and that he was at that monster's mercy and then he knew nothing. There was only oblivion that followed.

Alex stepped back and let the man fall to the ground. "He's alive. Good. Hopefully he'll stay that way for a few days. If he survives the early mutations everything should be fine." As the Strike Team came into view, Mercer paused, a small doubt troubling him. "No, this is the best way. To many risks with any other course of action. We can't risk Firebreak again."

"Red Crown, this is Tornado One! We have visual on Mercer in RZ Grid three-four. Looks like Ninja Three-Three is terminated. Transport is scrapped and we see no surviv-hold on... We've got a Marine moving down-HOLY SHIT!"

Alex had chosen to leave as soon as Heller began moving again. The panicked shouts and cursing of Strike Team pilots almost convinced him to smirk as he sailed straight through their formation before changing direction and vanishing from their sight around another building.

"Red Crown, Mercer has left the area. Should we pursue?"

"Negative Tornado One. Stay alert and hold position. Medical and containment teams are inbound to recover the survivor and confirm the status of the rest of the squad."

"Roger Red Crown. Strike Team holding position."

James rolled onto his back and stared into the sky, ignoring the gunships hovering above him. All his thoughts were now questions floating in his barely conscious mind. Why had Mercer let him live? What had he done to him? What was Alex Mercer? More and more questions flickered in his awareness before he lost consciousness again, only moments before the medical and containment teams arrived.

"Doesn't look too banged up; no open wounds." One of the medics checked over the unconscious Marine while another noted details. The remaining medics were on the street below checking for other survivors. Suffice to say, they didn't find any.

"Okay looks like...aww shit. Containment, get over here; he's infected. The scan almost didn't register it; must be a new strain." As the medics backed off the GENTEK containment squad got to work securing the infected to be transferred to the Yellow Zone's primary research base.

First Chapter Finished.

Already partway done with the second chapter, hopefully I'll be able to upload it tomorrow if not today.

Any questions or comments are welcome, if you have the time feel free to review. This is, unlike everything else I've posted, a full story that I intend to finish myself and I hope it's worth the time and that those who read it enjoy it.