Disclaimer: I don't own Kingdom Hearts or any characters mentioned in any of the movies and games mentioned in Kingdom Hearts or this fic.

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Chapter 4

Smith's Return

Name of World TBA

The man hung up his phone and turned to face the three others who were recovering from the last blow. Two stood waiting his attack, the third was missing.

"Where's Thompson?"

"Behind you," Thompson answered. The man turned and saw the boy unconscious in Thompson's arm. Thompson smirked and stared back at the new comer.

"Do not move," Thompson continued raising a gun out of his jacket and putting it to the boy's head. There was a clicking noise, as the gun cocked.

"If you want you're friend to live."

"Then its best."

"If you leave now."

The man turned his head to face all three of the men. Then, without hesitation, he flew towards Thompson, who fell back in surprise, and grabbed the boy holstering him over his shoulder. Then he ran towards the unconscious duck and dog while the other three shot at him.

Each bullet missed as he ran until he finally caught the curiously oversized dog by the collar and ran for the duck. He ran along the wall taking cover amidst the various trash cans and boxes until he caught the duck and flew into the air. The three men watched as the newcomer flew into the sky and vanished from sight.

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Sora gave out a low groan as he slowly opened his eyes. The first thing that he saw was Donald and Goofy lying opposite him in a long hallway. Both of the two were out cold. Sora looked up down the hallway and saw one door at the end. From the other side came three voices, one familiar over the rest.

"I'm telling you they're not dangerous."

"And I'm saying they're still viruses."

"I don't know. They don't look like much of a threat."

"Are viruses ever?"

"Look, I'm not going to waste my time so that these things can get to us before we get to them!" the door opened and a woman with dark skin stepped opened the door and approached Sora with what looked like a smaller version of the gun blade in her hand. She stopped inches from Sora and raised the weapon to his face. Sora panicked as the weapon made a click. But another arm appeared and stopped her from pulling the trigger. The man from before.

"So you're awake," he said calmly. He stretched his hand and pulled Sora up. Then he turned to face the woman, "See Niobe, they're no threat."

The woman wore a red skin tight coat and pants and her hair was tied into multiple knots over her hair. She lowered the weapon and eyed the other two. The man the politely shook Sora's hand and said, "I'm sorry I could not introduce myself earlier. Those agents have been harder to destroy ever since they were upgraded. Anyway, my name is Neo."

"Name's Sora," he shot back.

"And I'm Niobe," the woman said as she examined the still unconscious dog. Neo signaled for Sora to follow him and led him into the room. The room was dimly lit except for a few windows, and some peeling paint to reveal a rotting wooden wall.

"Where are we?" Sora asked looking out the window to see a city similar to the one he saw when he fought Xemnas. Thousands of people went about their business unaware of what was going on.

"In the matrix, a virtual world programmed by the machines to hide the chaos of the real world," Neo stared out the window with a look of dissatisfaction. He reached for a device that was left on a table and pressed a button on it.

"Could you repeat that?"

"Neo, man!" the device said, "I think you should give them the pill."

"Why?"

"Because their not reading like viruses anymore. They're reading like blue pills."

"How?"

"I don't know. We saw some sentinels fly past a while ago so you better get out. The EMP is already on stand by."

"Alright Link. Tell Morpheus and Trinity I'll be out shortly." Neo pushed a button on the device and placed in his pocket. Shortly afterwards, Donald and Goofy came in with Niobe.

"Glad to see you guys are awake."

"Nice nap," Goofy said. Sora smiled to see the awkward duck and dog finally awake, but that smile faded when he saw Neo place three red pills and three blue pills down on the table as well as three cups full of water.

"What's this?" Sora asked. Neo waved his hands over the pills and calmly answered.

"These are two special types of pills. The red one will free you from this virtual "paradise", the blue one will wake you up in a bed. You can believe whatever the hell you want to believe."

Sora eyed each of the pills and grabbed the three red ones. HE tossed one to Donald and one to Goofy who clumsily dropped it. Sora then reached for a glass of water and took the pill.

"What's the going to happen?" Sora asked Neo who had picked up a phone on the same table and disappeared into it.

"Where'd he go?" he asked Niobe who was now watching the three with silent bewilderment. Sora looked down at his feet and saw a metallic goop slowly make its way up his body. He turned to Donald and Goofy who were also being eaten by metallic goop.

"Guys!" he cried as the cold wet goop slowly crawled up his face and into his mouth. He let out a cry but was silenced immediately. He opened his eyes and looked around. He was in a jar of red liquid floating on his back staring up at the sky. He felt a tube that was in his mouth and tried to pull it out. IT slithered up his throat until it was out and he gasped for breath while under water. He got up out of the liquid and saw he was in a tub that was connected to a huge tower. But not only him, there were thousands of tubs stretching around the tower as well as other towers he saw in the distance.

"What's going on?" he asked himself looking around for Donald and Goofy. A strange metallic contraption floated from tower to tower examining each of the tubs. He felt something in the back of his head. He reached back there to find that his hair had been shaved off. With that there was a long metal wire sticking out of the back of his head and all the down his spine. Then he noticed the wire sticking out of his arms and legs. He was completely without clothing.

"Where are my clothes!" he shouted so loud the device scanning the tubs slowly floated towards him. He watched as the metal contraption floated before him and a metal claw extended from beneath it. It wrapped itself around his neck and he felt the wire slowly be pulled out of the back of hid head. Once it was removed, he felt the other wires burst out of his body. He let out a scream that no one heard until a door opened behind him and the machine slid him threw. He fell through an immense system of pipes and he slid past many other openings that could only lead to where he was. After sliding for some time he fell out a hole into a pool of water where he saw Goofy struggling to swim while Donald swam around effortlessly.

"What took you Sora?" Donald asked, unaware of the large craft lowering from the horizon behind him.

"Donald," he said at the sight of the ship as three claws extended from the ship and lowered themselves to where the trio floated. Each of the claws grabbed someone different and raised themselves into the ship where they were met by four different people. Neo, Sora recognized instantly. There where three others; a woman with dark hair, and bald man with dark skin and another with a goatee and darker skin.

"Neo?" he said. Neo smiled at Sora and said, "Welcome to the real world."

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Zion

Sora looked at his new clothes, a raggy sweater and pants, as well as a boots that he normally disliked. He reached for the back of his head and felt a metal ring there that wasn't there previously. It felt odd to have the device in the back of his head.

"It takes some getting used to," Neo said as he came into the dark room with Trinity, both were carrying trays of bowls filled with a white goop.

"So you guys are from another world?" Trinity asked Sora, who had just explained to the crew of the Nebuchadnezzar where they were from.

"Yeah," Sora said gratefully accepting a bowl from Neo. Trinity had handed bowls to Donald and Goofy, who began to eat the food but spat it out as soon as the first spoonful entered their mouths. Sora shrugged and took a bite of the food, but spat it out as well.

"What is this?" he asked. Neo and Trinity smiled at each other before saying, "That's the initiation food to the newcomers on board the Nebuchadnezzar."

Sora wiped his mouth with his sleeve. Donald, who was wearing an old shirt, protested, "That wasn't funny!"

"A-hyuck, tastes like the food Donald cooks," Goofy added.

"Yeah, wait, what!" Donald answered chasing Goofy out of the room. The three laughed at the two who were still as silly as ever. Sora stopped and sighed, reaching into his pocket and pulling out the keychain that Kairi had given to him before Donald and Goofy took him back to Radiant Garden.

"Is that the good luck charm you were talking about?" Trinity asked. Sora nodded and looked up.

"I wonder if we'll get off this world," he said to himself as the thoughts of Riku and Kairi crawled back into his mind.

"What are the other worlds like?" Trinity asked Sora who came out of his trance. Sora looked up and saw her looking at the five shells that were clumsily tied together. She spoke more calmly, "Are they free?"

"No. See, there are creatures, called Heartless. They go from world to world stealing the hearts of everyone. Once they have the hearts, they go for the heart of the world. When they destroy it, the world vanishes."

Trinity sighed and shook her head, "I guess there's no such thing as peace then." The ship stopped moving and came to a halt as it landed on the ground.

"What's going on?" he asked. Trinity and Neo took the trays and left the room. Sora left the room to find Donald and Goofy. After some searching he found Donald who had cornered Goofy into a closet. Sora talked Donald out of destroying Goofy and lead them into through the ship into another room where seven seats lay open. Neo, Trinity, and Morpheus were huddled around Link who was typing something into the computer.

"This can't be right," Link said.

"Maybe's it's a bug?" Neo offered.

"No, this ain't a bug," Link answered.

"Hey guys? What's happening?" Sora asked the four. Morpheus turned to face them.

"We have a problem. There's a lot of people suddenly looking like agents. The problem is none of them are reading like one," Morpheus said.

"Maybe we should go in?" Trininty offered.

"No, too dangerous," Morpheus put in.

"Aww, where's your sense of fun, Morpheus?" Sora asked. Morpheus sighed and said calmly, "Fine. We'll go in."

After some preparation, the group was quickly plugged into The Matrix and appeared in the same rotting room as before. A phone rang that Morpheus picked up, "Operator?"

The Matrix

"Watch your back," he said as two cars appeared in the street below. Morpheus' clothes resembled that of Goofy's, while Trinity was dressed in a black trench coat. The group ran down the steps of the old building and stepped outside.

"Link sent us in far from whatever's going on so we'll be fine," Morpheus explained as they steeped into the cars. Trinity drove the first car where Neo and Sora were seated while Morpheus drove the second, Donald and Goofy riding with him.

The cars sped past the deserted streets driving around. There was nobody around, the streets were empty, cars piled on top of cars. Several newspapers blew in the wind. The car stopped abruptly in front of a crowded street.

"What's wrong Trin?" Neo asked. He looked ahead at the shocking site. Ahead of them, a group of men in blue uniforms wearing helmets and brandishing guns were being beaten by a group of men who all looked the same. The men resembled an agent minus the earpiece and the fact that there were more than three. Neo stepped out of the car followed by Trinity.

"Wait, uh," Sora said, as he followed them. Donald and Goofy flanked his sides and Morpheus rejoined Neo and Trinity. At the site of Neo, each of the men grabbed a man in blue uniform and pinned him to a wall. One man stepped towards Neo, hands in his pockets, a look of surest victory in his smile.

"Mr. Anderson, surprised to see me?" the man asked.

"No," Neo shot back.

"Then you are aware of it?" he asked.

"Aware of what?" Neo asked the man as he circled around Neo, Morpheus and Trinity.

"Our connection," he smiled evilly, "You look surprised to see me, again, Mr. Anderson. That's the difference between us. I've been expecting you."

Trinity took a step towards the man but was held back by Neo. Neo looked at the man and asked, "Why are you here?"

"I killed you, Mr. Anderson. I watched you die... with a certain satisfaction, I might add. Then something happened. Something that I knew was impossible, but it happened anyway. You destroyed me, Mr. Anderson. After that, I understood the rules, I knew what I was supposed to do, but I didn't. I couldn't. I was compelled to stay, compelled to disobey. And now, here I stand because of you, Mr. Anderson. Because of you, I'm no longer an Agent of this system. Because of you, I've changed. I'm unplugged. A new man, so to speak. Like you, apparently, free."

"Free?"

"I was sent to the Source to be deleted. Before I arrived I encountered a new anomaly, very much in nature like you, it did not correspond to the rules of the Matrix. It could bend of them at will and had an ability that I received when it manifested itself within me. It called itself Omega Z. It blocked the path towards the source and spent some time questioning me, before it tried to delete me itself. But something happened, something I could not understand. I do not pretend to understand its reasoning, but I do understand that it gave me a gift when it was destroyed."

At that several more of the same man piled out of the nearby buildings until they completely surrounded the small group.

"The ability to make copies," the man finsihed.

"Congratulations," Neo answered. Sora turned to face Donald and Goofy, a look of worry on his face, "Guys, we forgot about the virus!" he whispered.

"You don't suppose that Omega Z thing was it do ya?" Goody said.

"Thank you," the man said towards Neo. Neo, Trinity, and Morpheus each took a fighting stance while Sora, Donald, and Goofy summoned their weapons.

"Still using all those muscles except the one that matters?"

"You haven't changed a bit, Smith," Neo shot back at him. The army of Smith charged the small group of people who could tell at this point they stood no chance.

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In an alleyway, an old woman carried her groceries back to her apartment. She crossed the old alleyway, hearing fighting at the other end.

"Those hooligans," she said to herself, "If I'm lucky I'll be able to cross the street before they see me."

But she never crossed the street. Once she was at the end of the alleyway, she saw an army of men all dressed the same fighting six others who were well outnumbered. She dropped her bags and gasped, before she disappeared. In her place stood a familiar looking man; Agent Thompson.

"You," he said as he saw a rogue program approach him; Smith.

"Yes me," he said as he llunged his hand into the agent. The agent let out a cry as he slowly turned into a copy of Smith.

"Me…me…me," Smith said to himself.

"Me too," the copy of Smith said as he turned and entered the frame. Smith smirked and walked into the next street, ready to further his plans.

Author's Note: I'm procratinating studying. Yes I know, very sbad thing to do at this pointbut I got like three more years of this stuff ahead so no worries yet. As they say in other fics; read and review.