Disclaimer:

Tron and Tron Legacy and the whole fun franchise belong to Disney.

This is an AU where the page came a few weeks early and Sam is out of town.

Warning: This chapter contains mind rape.

User Rectified

Chapter One: Guinea Pig

"Sam?" Alan called out as he knocked on the door to the garage that served as the home for Sam Flynn. Alan had been over to visit with the youth several times before. He was even been given an extra key to the place in case Sam took one of his sabbaticals and needed someone to get the mail and to take care of his dog, Marv.

Alan usually would have called before coming over but he had just received something that he could not believe. He received a page on his old pager That Kevin Flynn had given him years ago. What was amazing was not the fact that the pager still worked but the fact that the number that reached him had long been disconnected.

"Sam are you home?" Alan asked. This was unlike Sam. He would have let Alan or Lora know where he was going if he did go on a trip so they could make arrangements. This also worried Alan. Something could have happened to his young friend

Using the key, Alan unlocked the door and stepped inside. "Sam?" He called out again as he walked through the place and noticed something else that was a bit unusual. He didn't hear Marv bark. He couldn't even find the dog. Alan felt his heart beat increase as he frantically walked around, trying to find some sign of Sam. He noticed the Ducati was left behind.

Alan took a deep breath and sat down. His hands were shaking out of fear. He had to call Lora. As he fumbled for his phone he noticed a folded piece of paper on the coffee table. He grabbed it and unfolded it. There was a message written by Sam.

"Hey Alan, sorry about not telling you sooner. Dave and few others invited me to go camping with them. I took Marv with me. He'll love the great outdoors. I'll be back in a few days. Feel free to take the bike out for a ride. She gets lonely if she isn't ridden on. "

"Just like his father," Alan sighed and sat back and remembered the similar stunts that Kevin had done. He set the note down and placed the key to Flynn's Arcade down on top of it. It was the original key. Alan had the second one. He decided to investigate the source of the mysterious page himself, but first he should call Sam and tell him the good news.

"Sam, this is Alan." He gave the youth the greeting once he reached the voicemail message. "I received a message on my old pager. It came from your father's office at the Arcade. I'm going to check it out. Call me when you get my message."

There was no one in the old office that had once doubled as an apartment for Kevin at the top of the Arcade. Alan had searched through the entire place and came across noting, no sign of life save for a few roaches and spiders.

"Should I tell Sam?" Alan asked as he stared at his pager. What was he going to tell Sam? That he received a message from the office but there was no one there? He was going to bring up the kid's hopes to only have them come crashing down. No. He was not going to tell Sam anything until he found out what had caused the message to reach him.

Alan felt a chill crawl down his spine as he walked through the arcade and stared at the games that were covered in plastic sheets. He remembered when it was full of lively teens popping in quarters and playing the games. He also remembered when he and Lora walked through the place in search of Flynn that fateful night when Dillinger had cut of access to his Tron program. The place seemed so haunted now.

His eyes fell on one of the machines against the wall. The neon overhead had spelled out TRON. Alan could not help but to smile. After they had destroyed the MCP Kevin had called Alan Tron, after the security program that Alan had created. Kevin had seemed to take a great liking to Alan's creation. Kevin developed a game named Tron and with the game there was promotional material including a poster and action figures.

"You were one of my best creations," Alan said as he removed the plastic from the machine. He had given the program to Kevin for a special project he was working on but never saw sign of him again. Him? Tron was a thing, not a person. Alan had no idea why he was thinking like that.

"I'm losing my mind it seems," Alan chuckled and shook his head. "I'm talking to myself for starters." He stared down at the ground and noticed curved groves and scratches as if someone was moving something heavy around and the nearest heavy object was the game.

Alan gave the machine a small push and it moved with ease, swung out as it were built to be like that. He looked behind it and saw a door in the wall. The machine was blocking a secret door.

"Flynn, you were always a sly one." He used a small pocket flashlight after he opened the door and went down the stairs to another room.

The place was set up as a second office, a secret office. The beam from Alan's light danced off the walls and the furniture. It found the old electronic game that Kevin had been playing with when they formed the plan to hack into ENCOM nearly thirty years ago. The beam moved over to a cork board that held Flynn's notes and family pictures. There were many of Sam and Jordan and a few of Alan and Lora.

"This was wear you were developing that secret project of yours?" Alan asked as he made his way to the desk. After mopping away the dust, Alan could see that it was a touch screen computer desk. "Backdoor and Whoami?" Alan read. He was about to type in how own name, but Kevin Flynn would not answer to Alan Bradley. He typed in Flynn.

The screen changed, asking Alan if he wanted to initiate the previous command.

"Kevin's last command? Well of course I do." He typed in a Y.

"Activate laser?"

Alan's finger flew to the N. Why would he do something ridiculous and stupid like that? But if that was Flynn's final command and if Alan wanted to learn about what happened to his friend and why he had received page he was going to see what happens if he activated the laser. Again he pressed Y.

There was a sharp whistling in his ears and then it suddenly stopped. Alan blinked. There was a strong ozone scent in the air and the screen of the computer went blank. He spun around in his chair. Everything in the room was different. There was less furniture than before. The couch had different upholstery and the electronic game was gone.

The pictures on the corkboard were also different. There were some of Jordan, Sam, Alan and Lora but a few other pictures of different people. There was one of a woman that Alan had never seen before. "Ophelia-the first ISO." Was written under it. There were a few of Kevin and Alan, except Alan did not remember the last time he wore such getup. There was also one of himself and two Kevins. "Me, Clu and Tron." Was written underneath it.

"What in the world?" Alan asked as he leaned in closer to study the picture. All three men were smiling. One of the Kevins had his hair slicked back and the man that looked like him was smiling. His hair was the same as Alan's was back in the early 80's.

Alan had no idea what he was going to find as he searched upstairs. All of the video game machines were gone. The arcade was even more empty than it was before. The upstairs office was as just as empty. After he came down the steps he had to wonder how everything looked on the outside. He stared through the glass doors.

The whole city was different. The regular buildings were replaced by dark buildings in unique geometric shapes and framed in bright glowing neon.

The sidewalk and street in front of the arcade was filled with glowing light that was able to enter through though the glass and cover Alan. He had to shield his eyes from the light and as he squinted he could make out something landing. He had to blink several times when he realized what it was. It looked just like a recognizer straight out of Space Paranoids.

Despite the warning signals going off in his head, Alan did not move, nor made any attempt to run. Even if he had, where could he have gone? He watched as the midsection of the recognizer lowered itself to the ground and several figures dressed in black and glowing red circuitry stepped off and walked straight to the arcade.

"Program, identify yourself." One of the soldiers said to him.

"I'm not a program," Alan said. "My name is Alan Bradley. Where is Kevin Flynn?"

"Bring him aboard," another soldier said. "Jarvis will know what to do with him."

Jarvis turned out to be a strange pale man that had a glass shield mounted on his bald head. He listened to what Alan had to say and after he gave him a good look over gave the order for Alan to be suited up and taken to the glorious leader.

The following twenty minutes went by a whirl to Alan. First he was hauled below ground, where four lovely young women stripped him of his clothes, including his glasses. He was covered in a strange dark material that covered itself in odd armor with plastic like padding, flexible mesh and a few glass like pieces that lit up almost instantly. The last thing they did was place a shiny black disk on his back. Once it became synched with him his vision became clear.

He had to get a good look at himself. He had a slender vertical light on each knee and at the top of each foot. Looking at his arms he could see similar lights on center of the arm at the joint. The lights on his gloves seemed to be illuminating the bones of his index finger, middle finger and thumb. There were four smaller round lights on his stomach. Two of them were just above his pelvic region and two others were above his naval. There were two dashes close together above those. He would probably need a mirror to have a better look at himself.

"Just like him," Jarvis said when he took one glace of Alan's new look. He turned to the soldiers. "Take him aboard."

"Where are you taking me now?" Alan asked as he was being led into another Recognizer.

"We are going to see the person that you wanted to see." Jarvis answered. His mouth turned up into an smile that did not sit well with Alan.

Alan was taken to a large room at the top of a building. There was a someone sitting in a chair dressed in black and golden-orange neon. A helmet had obscured his face

"Look what we brought," Jarvis said as soon as they had stepped inside.

The figure said nothing only nodded at Jarvis and pointed to the door.

Jarvis nodded. "We will return when you summon us." He lead the group of soldiers out of the room.

"Who are you," Alan asked as the figure stood up from his chair and made his way to him.

"Alan Bradley," the figure said. His voice sounded like a distorted Flynn behind the helmet. "It's me." The helmet melted away, revealing the unaged face of Kevin Flynn.

"Kevin?" Alan asked in disbelief.

"Yeah," Kevin answered. He looked exactly the same as when he had disappeared. His mouth set into that familiar smirk of his and a bit of stubble on his chin. The only difference was that he had his hair slicked back.

"It's you," Alan gasped as he placed his hand's on Kevin's shoulders. "It's really you."

"It's me and it's you and your are here." He sounded happy to see Alan but his enthusiasm seemed fake. "Although you have changed."

"I've gotten older." Alan continued to study his friend's face. There was something off. "You haven't changed."

"We don't age here." Clu stroked Alan's face. His fingers brushed against Alan's cheek. "You are older but still pretty." His smile grew wider as he grabbed Alan's chin firmly.

Alan chuckled as he stepped away from his friend. "That's the Kevin Flynn that I remember, always a joker. Everyone is going to be pleased to see you, especially Sam. I tried to tell him about the page but he wasn't at home. I left a second key for him."

"Sam," Kevin repeated and blinked. "My son."

"Yes." Something was wrong. The Flynn he knew would have asked about Sam as soon as he laid eyes on Alan.

"He's all grown up." Clu closed his eyes. "I wished I could have been there to see it. Does he know about this place?"

"I left him a message and an extra key." Alan wasn't certain why he was telling him this. "But that doesn't matter. We should get out of here. When he gets home from his trip he will be ecstatic."

"I can't go."

"Why not?" Alan asked. "You seem to be running the place. You are not a prisoner here, are you?"

"I am in charge."

"Then why won't you come back with me?"

"I want Sam to come here so I can show him everything."

Alan took another step back away from him. "You are not the Kevin Flynn that I remember."

Flynn shook his head. "No I'm not." He pressed something on the arm of his chair before he walked back up to Alan. "I am called Clu."

"You're a program." The writing under that one picture made a lot of sense. "Where is Kevin? Where is Tron?"

"Tron?" Clu asked and seemed to be trying to keep himself from laughing. "He's around as for Kevin Flynn? Your guess is as good as mine, but Sam is going to help me find him."

"Sam?" Alan asked as Jarvis and several guards returned to the room. "What are you going to do with Sam?"

"He is going to serve his role as bait." Clu said as he ran his fingers down Alan's chest. "That was your original role but Sam will play it better." The tips of his fingers pressed against the lights on Alan's suit. "You have been given a new role. Alan Bradley, you are going to help test a theory of mine and if it succeeds then we are going to have a great deal of fun."

"What if it doesn't?" Alan asked.

"You better hope that it does."

Once again Alan found himself aboard a Recognizer and was taken away towards some alien place, or alien in his mind. Clu and Jarvis rode with him.

"What is this theory?" Alan asked they continued to ride through the sky.

"Something that will benefit my goals," Clu answered as he once again ran his finger along Alan's chest.

"What are those goals?"

"Perfecting the world." Clu's finger stopped on the strange symbol on that rested over the center of Alan's clavicle. The symbol was that of a broken letter "A" and another slender vertical dash underneath it. "I will make you perfect."

"I am happy with they way that I am."

"Perfection does not depend on your happiness, Bradley." He narrowed his eyes. "You will be my first User to perfect. My first one."

The Recognizer docked at a large Ship. The guards brought Alan to a row of black chair like contraptions that remind Alan of massage chairs.

"Put him in," Clu ordered.

Alan was placed with his face and chest against the padded back of one of the odd chairs. He felt his arms and legs being fastened in with restraints and something press around his head like a circlet covered in a leather like material.

"Give me his disk."

Alan heard a small snap. "What are you going to do to me?"

"I already told you my first User. I am going to help you. You are an imperfection and I will fix that."

Alan tried to thrash around but the restrains held him fast.

"I wouldn't try that during the process if I were you," Clu told him. "Now put in his disk. We need to get it lined up with what User's have for a code."

Alan wasn't sure what was going on until he heard the hum of the machine starting up. Then the pain hit. It felt like sharp needles being inserted into his brain. Images flashed before his eyes. All of them were of his past. He could see his marriage to Lora, the birth of his children, family trips they had taken, the parties they have attended. His children's graduation, his graduation from high school and college, when he first met Lora, and Kevin, everything came back before his eyes.

When he came to some his earliest memories, those that were not as clear as the others a new pain had struck him. The sharp needle like pain appeared dull compared to this. It was as if someone took a carving knife and sliced it through his mind. He watched in horror as some of those older memories melted away. More images were fading. It wasn't just images. His actual memories were being torn away.

"Stop it." Alan shouted as he thrashed around. "Don't take them away."

"They need to be taken away," Clu told him. "They are impurities. They are what are standing in the way of your perfection."

"The love for my friends and family are not an imperfection." Alan screamed as he fought to retain his memories. He continued try and tear away from his restraints fought to retain his memories until he was exhausted.

"He is getting too weak," someone said.

"Stop the process and energize him," Clu ordered.

The pain and the images stopped and Alan felt liquid against his lips. He hadn't realized how thirsty he was until he had started drinking. It tasted so fresh and pure and he felt his strength returning to him.

"Proceed," Clu instructed again.

The pain and the images returned and Alan used every bit of strength to retain hold of his past. When he became too weak he was given more of that liquid to drink and they exhausted him to the point where he could not resist the beverage.

When more intimate images appeared of him and Lora, Alan felt a new sensation as if fingers were brushing against his inner thighs. The fingers slid higher until the pressed against his center causing Alan to feel uncomfortable and yet also aroused.

Alan screamed but the groping and rubbing continued. Images of Lora going down on him appeared and the painful slicing was accompanied by the image of Lora melting away and replaced by Clu with a look of ecstasy on his face as he pleasured Alan. That was false. Wasn't it? He could remember how Clu had given him so much enjoyment. He remembered how warm and soothing the program's tongue was when it flicked against his cock.

"No," Alan shouted. His real memories were being removed and replaced by false ones.

"Greetings, program," Kevin, no not Kevin, it was Clu appeared in his head. "Welcome to the grid. I have created you and your brother to be the finest security programs."

"I'm not a program!" Alan shouted. "My name is Alan Bradley. I was born in 1950. I married Lora in 1982. We have a son named Jethro."

"Stop fighting," Clu told him. "Embrace your perfection."

"Never." Alan said as he struggled against his restraints and more memories were being sliced away and replaced with false ones. He fought until he was too weak, only strong enough to sip his drink and the nightmare would begin again

A/N: I can't remember if I've written something like this before. Inspired by the multiple requests at the Tronkinkmeme at Live Journal using the Alan/Clu Pairing.