A/N: This story is a crossover of Half-life and Resident Evil. The Raccoon City outbreak in this story uses the timeline of the movie Resident Evil: Apocalypse. Please please review, I have my cookie set to accept anonymous ones so that even readers who are not members of fanfiction can do so. I really hope you enjoy.

Project: Matrix

Chapter 1- An American Warzone

Subject: Nathan Sheffield
Male, age 23
Training: United States Marine Corps, Special Forces
Rank: Corporal
Current Assignment: Hazardous Environment Combat Unit, Santego Military Base, Arizona
Mission: Classified

Black Mesa Research Facility
Black Mesa, New Mexico

Corporal Nathan Sheffield had been trailing Gordon Freeman since he had stepped off the Osprey. He was not about to give up and let his fellow Marines deaths go unpunished. He was going to avenge his comrades, the same comrades that Freeman had killed. Even his best friend had fallen before the mad scientist, supposedly the first of his victims.

Nathan Sheffield was usually a happy-go-lucky guy, but he truly hated Freeman for killing his friends. They were good Marines. Nathan knew what his orders were, to silence the facility, kill everything that wasn't wearing camo and a P.C.V. He also knew he should at least try to see things from Freeman's point of view, that he was just trying to survive. But in Sheffield's eyes, that didn't constitute running around in full bulletproof body armor and killing everything there was to kill. Freeman knew good and well he wouldn't stand a chance without his H.E.V. and he was taking full advantage of it.

No matter how Sheffield looked at it to see how Freeman was thinking, he just couldn't excuse the fact that he had an advantage and he was using it to kill his friends. He wanted to see things from the scientist's perspective, but he just couldn't. He didn't want to kill anyone and he never had before, but if someone was going to die by his hands today, it would be Freeman.

Now Sheffield's team was moving through sector one making their way to Black Mesa central command. Apparently they were under heavy attack and needed assistance.

Three aliens teleported right in front of Sheffield's team and they immediately mowed them down with their MP5's. They moved on and came to a cross section with the hallways. They heard gunfire from what sounded like a pistol. Sheffield put his hand up and signaled them to stop. The four soldiers heard a cry from what sounded like an alien.

"Sheff!" hissed Berkley, one of the members of the team.

Sheffield looked over. Berkley was crouched next to the wall with his back against it. He put two fingers to the green lenses of his gas mask and pointed around the corner. Sheffield leaned over a little bit so he could see.

A security guard took a dive and just avoided the powerful tail of one of the alien lizards. It was futile for the fact that he was attacked by a Headcrab and the lizard smashed him into the wall turning both the alien and the guard into a bloody mess on the wall. Berkley and another member of the team, Nelson, quickly moved around the corner and opened fire. The lizard saw them and tried to spit its acid at them but the two soldiers killed it before it could harm them.

"Delta two-four, come in."

"Delta two-four here." said Sheffield into his radio.

"Change of plans. Get back top side and rendezvous with Delta three-nine and secure sector seven, over."

"Rodger that, orders received." He clicked the radio off and pushed past his team. "Let's go, it sounds like they are having a tough time."

The marines stepped off the elevator and were nearly hit by a blast from one of the aliens. The other members of the team ducked down and fired back. Sheffield tossed a grenade behind a brick wall and saw a gory alien body fly out from behind it.

Nathan led his team across the hangar and out into the open. They could hear gunfire and jets flying overhead. The whole Black Mesa campus had been turned into a war zone. Sheffield wondered why they had been sent in; these were American citizens after all. He was pretty sure there was something in the Constitution that made it illegal to use military troops against American citizens.

He dismissed the thought and kept his focus on the mission at hand. It was distractions like that that got people killed, especially him and his team. Sheffield would prefer to get out of here alive. When he had joined the Marine Corps, he hadn't expected to actually get thrown into a combat mission, much less one that meant fighting hostile aliens. He had joined to pay for college and to see what it was like to handle actual guns.

Sheffield came from a very protective and wealthy family. He had joined the Marine's eager to get rid of his 'spoiled rich boy' reputation, which he hated to no end because he tried very hard not to be snobby and act like he was better than everyone just because his parents had money. He had also wanted to see the world.

Now he was killing things, but not even out of the country. He was standing here, on American soil, in the New Mexican desert, trying to survive a in a self inflicted war zone.
The team made their way across the warehouse and out into the open where a covered truck was parked. Blood was spattered all over the windshield and the passenger's body was half hanging out and bleeding all over the ground. The driver looked as if he had been pulled through the window and left there.

Sheffield made a hand gesture, signaling Berkley to scout ahead. He did as he was told and moved toward the truck sweeping his gun around looking for threats. Berkley made it to the truck in one piece and signaled for the rest of the team to follow. Sheffield led Nelson and Klive to the truck.

"I saw something; it looked like a security guard. He ran across the parking lot and disappeared into that door." whispered Berkley to Sheffield.

"Leave him, we need to get find Delta three-nine."

They cautiously moved down the road occasionally passing overturned and burning trucks with bodies of their comrades lying around them. They even passed a wrecked tank with flames flickering from inside. The team eventually came to a thick metal blast door and radioed in.

"Delta two-four to command. Come in."

"We read you two-four, report your status."

"We've reached the entrance to sector seven, but the blast door is locked."

"Rodger, I'll try to raise two-nine on the radio, stand by." There was a brief pause and the radio operator came back. "I'm not getting a response, see if your engineer can hack the controls." "Rodger that." Sheffield clicked his radio off and turned to Klive, the engineer. "See if you can get the door open."

"Yes sir." said Klive as he pushed past the other Marines.

Klive used his knife to pry open the metal wall panel and began to examine the wires that made the key pad work.

"Uh, sir?" Sheffield looked up and saw Nelson staring down the road.

Nathan took a couple of steps to the side and saw what Nelson was worried about. A column of aliens was making their way past the small alley the Marines were in. "Work faster..." he started to say to Klive.

Before he could finish his statement, a green lightning bolt zipped past his head and turned the steel behind him into a molten hole. Nelson opened fire finally realizing the aliens had noticed them.

Sheffield did the same and several of the aliens fell to the ground. Unfortunately all the commotion caught the attention of the other aliens and they turned to shoot their bolts. Nelson dove to the ground and narrowly avoided an energy bolt. Sheffield dropped to one knee and kept firing at the monsters. Berkley finally joined in with his SAW.

Klive frantically worked with the wires trying to get the door open while Sheffield, Berkley, and Nelson tried to give him more time. He cut and skinned various wires and tied them together trying to get a current going and the right combination in. He finished twisting the last wire and tapped a few buttons on the keypad.

The door started to slide open and suddenly stopped about two feet apart. He looked at it and figured it was enough room for them to get through.

"Go! Go! Go!" he yelled above the gunfire.

He slipped through the crack in the door and saw Nelson take a direct bolt in the chest. He flew back and landed on the ground just in front of Sheffield. Berkley started back but kept firing and covered Sheffield as he grabbed Nelson and dragged him through the door. Berkley fired the last of his magazine and sprinted to the door.

Klive hit the buttons to close it and an alien tried to get in but was too late and the doors squished it. The soldiers heard clawing at the heavy metal and knew they had made a narrow escape. Sheffield turned his attention to Nelson and quickly kneeled down. Berkley did the same.

The energy had burned through his Powered Combat Vest, or PCV, and into his flesh. His eyes seemed not to focus on anything and none of them had the training to help him considering he was them team medic. A pool of blood started to form around him and Sheffield cut the straps to his vest with his knife and pulled it off.

Nelson's normally urban-camo shirt was drenched in blood and in the middle was a burn mark where the fabric seemed to have melted to his wound. Blood was leaking down his side. "Morphine..." he managed to say. Sheffield searched Nelson's vest pockets and found the morphine. Nelson was shaking uncontrollably and Berkley was doing all he could the keep his head off the ground and his hand on the wound. Nathan stuck the small morphine needle into his shoulder and squeezed it dry. He knew Nelson couldn't survive a wound like that, but he did know it was his duty to make him as comfortable as possible. "Get... out of... here..." he gasped. His shaking slowed and his muscles gradually relaxed. "Alive." he finished with his last breath. Nelson stopped moving and his eyes focused on a fixed point.

Sheffield closed his eyes behind his mask and exhaled. Berkley reached over and closed his eyes. Sheffield opened his eyes and ripped Nelson's tags off his neck and pocketed them.

He stood up and took off his helmet and mask. He hated the masks. They made it extremely hot. The cool air hit his face and dried his sweat. He savored the feeling of the cool air hitting his sweaty face, trying to forget one of his team mates had just died.

Nathan Sheffield was a good looking twenty-three year old. Right now his face was obscured by dirt and grime that had somehow made its way under his mask, but normally he had smooth skin and a slightly rounded face. He had short light brown hair and he looked out at the world through deep blue eyes. His muscular chest was hidden under his black and dark green PCV and urban style fatigues. His hands were covered in fingerless gloves and his shirt sleeves were sloppily rolled up to his biceps partly to make it easier to move and partly because it was ninety-three degrees outside and it made it cooler even though his vest had a next generation cooling gel that helped keep his body temperature down.

He placed his helmet and mask in his heavy olive drab backpack. He hadn't noticed it before but Klive had been standing there the whole time watching them tend to Nelson. He pushed past Klive and exchanged a look of disgust and remorse with him silently telling him that he was a coward.

Klive looked down and shut his eyes for a moment. "Lets go." said Sheffield tartly.

Without another word, he walked down the hall and Berkley followed behind him. Klive took one last look at Nelson and followed Berkley. The team walked on for a while without a word and finally Sheffield stopped to radio in. "Delta two-four to command."

"Command here, we read you Delta two-four."

"Command, we have entered the compound and there is no sign of Delta three-nine."

"Sir!" yelled Berkley from behind a corner.

"Stand by," said Sheffield into the radio. He ran over to Berkley and looked where he was looking. Two members of Delta three-nine were lying on the ground in a pool of blood. "Scratch that. We found the remains of Delta three-nine. They are dead." There was a pause.

"Rodger that. Your new orders are to find a way into the old teleportation labs and keep the occupants from escaping. We believe there are enemies in there and are trying to use it to escape. Under no circumstances are they to leave."

Sheffield listened and knew they meant security guards and scientists. "Lethal force is authorized." Nathan exhaled and shook his head.

"Yes sir." He turned to Berkley and clicked off the radio. "You hear that?" he nodded.

"Can't we just detain them?" "I plan to."

"Those aren't our orders." said Klive. "Shut up. You didn't listen. They said lethal force 'authorized'. Not that we need to." replied Sheffield.

He was happy to see that Berkley had some sort of human morals, even if it was against their standing orders.

A loud crash came from a small room behind Berkley and he turned around. A human form with some sort of creature attached to its head came lumbering out. His pants had the urban pattern that told the Marines he was one of the Delta three-nine people. The second one followed him out and they started toward the Marines.

Berkley opened fire with his SAW and tore the first one to shreds. Just as the human-alien went down, the machine gun jammed and Berkley started trying to fix it. He didn't notice the creature take a swing at him with its tentacle-like arm. It impacted on his shoulder and sent him flying into the wall. Klive threw himself at the creature to give Berkley a chance to get up and also to show he wasn't a coward.

Nathan took the chance to raise his gun and realized it had one bullet left in it. He noticed a small rat-like alien crawling toward Berkley. It threw it's self at him and he put his arms up to stop it. It was trying to reach his face. Sheffield turned and fired the last bullet of his clip into the Headcrab and watched Berkley throw it aside and continue to try to un-jam his gun.

Sheffield dropped his MP5 and ripped out his Desert Eagle and clicked on the laser sight. The human-alien creature flung Klive against the wall, shattering his skull and killing him instantly. Nathan saw the red dot appear on the creatures head. It turned toward him and took a step. He hoped to god that the human inside was dead and he wouldn't be killing anyone. The zombie took another step and lunged at him.

Sheffield squeezed off a shot and kept pulling the trigger. The alien that covered the soldiers head exploded in a flurry of yellow blood and gore. The body collided with him and they both fell to the ground. Sheffield rolled the body off him and got up. He holstered his pistol and walked over to his MP5.

Berkley finally got his gun un-jammed and was seeing to Klive.

"He's dead." he said as Sheffield picked up his modified MP5 and inserted another clip.

Berkley hated to do it, but searched Klive's body for supplies and found four MP5 magazines. He tossed them to Sheffield who put them into his vest pockets. Berkley also tossed him two of the three grenades that had been Klive's.

Sheffield led Berkley down the hall that led by the room the human-aliens came out of. They followed the hall and eventually came to a room with a large elevator in it. Berkley saw a stationary radio on a table and a shot gun next to it. He walked over and inspected the shot gun before slinging it over his shoulder.

Sheffield of course went to the radio and turned the frequency knob until voices could be heard calling for backup and giving orders.

"It's Freeman! He's coming down the-" the Marine was cut off by a burst of gunfire. More gunfire erupted in what sounded like their comrades going at it with Freeman. "Send back up! Freeman is tearing through us-" "Stop him! Stop him!" "The suit! We can't get through the suit!" "Fire in the hole!" they heard an explosion and more gunfire before all went silent. "He's in the rail tunnels! Cut the power-"

Both Berkley and Sheffield knew what had happened. Gordon Freeman had once again torn through the Marines and survived to slaughter another group of them.

"It's kind of depressing. Hearing them call for us to help and knowing we can't." said a voice from the doorway. Sheffield spun around, his gun level ready to kill anything. Berkley did the same and they realized it was a Marine that had said it. "Corporal Sheffield I presume?"

"I am, and who are you?" Corporal Mathews, Delta three-eight. My team is making sure the perimeter is secure, they will be here momentarily."

"I didn't know command was sending another team to help us. How did you get in?"

"There have been reports from this sector about some security guard killing our men, and doing a damn good job. Apparently he's helping Rosenberg and the others escape. We got in through the old tunnels beneath this building. We got lucky and found a small elevator that led right up into the offices. We just had to break through a few badly done repairs." he finished. "Where is your team?"

"Dead." Sheffield replied. Five more Marines entered the room.

"It's all clear sir. There are a few fresh bodies but most of it's clear."

"That would be my team." said Sheffield. The Marine that had just reported turned and noticed Sheffield and Berkley standing next to the radio. "Sorry sir."

"Did you get the name of the guard yet?" asked Corporal Mathews to the Marine that had just walked in.

"Yes sir. Uh," he looked at a small piece of paper. "Barney Calhoun. He's worked here for three years and had a spotless service record. Missed one day for sick leave in all that time."

"Good work." said Mathews. The Marine nodded and took a seat next to Sheffield at the radio. He was one of the soldiers wearing a mask just as Sheffield had been doing earlier. Mathews, however was wearing a red beret instead of a mask or helmet. "Are you ready to go down and hunt some scientists?" he asked every one in the room. Mathews' squad let out a "hurrah!" and he turned to Sheffield and Berkley. They merely nodded and stepped into the elevator.

The small elevator descended to the floor below revealing a large room with alien and security guard bodies strewn everywhere. Blood was on the walls and floor and it immediately became obvious that a battle had taken place in the large room. The elevator came to a stop and the soldiers stepped off onto the bloody floor.

Mathews' team moved across it sweeping their guns around and making sure there were no hostiles. Once they were sure it was secure Mathews took point and led the soldiers into the next room.

Berkley moved to follow them but Sheffield held him back until they disappeared around the corner.

"With them here we can't keep those people alive. We have to warn them that they are coming." he told Berkley.

"That's treason there." replied Sheffield. "But your right. We can't let them be murdered like animals."

"How do we get there with out running into him?"

Sheffield looked around and found a vent about three feet above the floor. He walked over to it, drew his combat knife, and pried it open.

"It'll be a tight squeeze, but we should be able to fit."

"Where does it lead?"

"Dunno, but we're going to find out." he said as he re-sheathed his knife and pulled himself into the small space. He crawled and heard Berkley put his gun in and lift himself into the vent also.

"Now I know what a TV dinner feels like." Berkley recited.

"I hate that movie." said Sheffield.

"Are you kidding? I love that movie. Bruce Willis is awesome."

Sheffield suddenly stopped and Berkley nearly ran into him. Sheffield looked down through a vent and watched Mathews' team go right under them and look around.

"Where is Sheffield?" he asked.

The Marines looked around and finally realized that Berkley and Sheffield were missing. Nathan looked back at Berkley. "Did you close the vent?" he mouthed. Berkley looked at him trying to understand what he was saying and finally realized it. He started backing up quietly toward the opening they had come out of.

Mathews reached for his radio and Nathan realized he was going to call them. He quickly reached for his vest and struggled to free his handheld radio from the pocket it was in. Mathews clicked the radio. Sheffield freed it and clicked it off just as Mathews spoke.

"Mathews to Sheffield, come in." he said. Sheffield exhaled and heard Berkley come up behind him. He looked back and Berkley nodded. "Mathews to Sheffield, come in." he said again. He waited for a response and finally signaled for his team to go ahead. "Sheffield, if you get this, meet us at the lab entrance." he said into his radio before walking away.

Nathan quietly exhaled and continued crawling through the cramped ventilation shaft before finally coming to an exit. It was blocked by a heavy grate and as far as Sheffield could tell it was at least a fifteen foot drop to the floor.

He smashed his shoulder against the grate as hard as he could and looked at it. All he had done was dent it. He slammed into it again and again until he heard it start to give away. He rammed it one last time and sent it clattering to the floor.

"Hold my feet." he said to Berkley.

The Marine grabbed his ankles and helped Sheffield inch out of the vent until he was hanging out against the wall. Sheffield put his hands up above his head and braced for the fall. "Drop me."

Berkley let go and Nathan plummeted through the air before landing hardly on his braced arms and falling over onto his back. He rubbed his forearms and got up, bringing up his MP5 and sweeping it around the room.

"Are you okay?" asked Berkley from the vent. Sheffield finished looking around the room before replying.

"I'm fine. Wait there, let me find a box or something."

"Right." said Berkley.

Sheffield walked across the room, keeping his gun leveled.

The room was not small. It looked like a warehouse; boxes of all size and shape filled the room and were stacked to the roof against the walls. Parts of the storage area had so many boxes stacked that it was like a maze.

Sheffield looked around for a fork lift or something he could use to help get Berkley down without breaking his neck. Nathan knew he was lucky he didn't break his neck from the fall, that all he got was bruised fore-arms.

He spotted a bright yellow fork lift in the corner near a stack of heavy boxes and jogged over to it. The body of a worker was hanging half out of it with his head drooped and blood all over the floor. His normally bright orange jumpsuit was crimson now and he had a hole in his chest as if something and taken a bite out of him.

Sheffield pulled the body out and onto the floor. Surprisingly there was no blood on the seat or controls. He sat down, and quickly dismissed the eerie feeling that the man had been sitting where he was when he died.

He started the lift, got a feel of how it worked, and drove it over to the vent Berkley was in. Sheffield raised the fork up to the vent and Berkley climbed onto it. Nathan brought it down and Berkley hopped off. Sheffield turned the lift off and got out.

Berkley got out his PDA and activated the map. The President had authorized a satellite to be used specifically for this mission along with four AWACS and if necessary, two tactical nuclear warheads. The satellite was to help pinpoint soldiers locations within the facility by the tracking devices in their PCV's so they could pull up the map if they got lost and be able to find a way out.

"The old teleportation labs are right below us."

"How do we get down?"

"There should be some sort of service elevator somewhere outside this warehouse."

"Which way?"

"Um, east." he said pointing toward the maze of boxes. Sheffield sighed.

"That's great. We better get moving if we're going to beat Mathews to the labs." he said and made sure his gun was going to work if he needed it.

Before they could say another word, a small alien appeared from the maze of boxes and stopped. It was small and looked like its mouth was its entire head.

The creature chirped and squeaked happily upon seeing them. Sheffield raised his gun and aimed, but held his fire. Berkley flipped through the pictures of aliens on the screen of his PDA.

"Uh, it's called a 'Hound-eye'." he said.

"Is it a threat?"

"Only if it perceives us as one to it."

The small creature hopped toward them and stopped about five feet away. It looked as if it were surveying them. Sheffield gripped his gun tighter and the alien just looked at him. It stared at him for a moment and then turned and hopped away.

Both of them let out a sigh of relief and started toward the maze of boxes.