Sam Flynn stands facing a large glass window. It was dark and gloomy outside. Rain fell from above. Clouds hid the moon from view. Sam had come to expect this kind of atmosphere. He had to sit through it everyday since he took back his father's company. He looks down at a necklace that hangs around his neck. This wasn't just any necklace however. This was a microchip containing one of the most technically advanced worlds. But Sam was only one who knew this (except for a few others). He did not share The Grid with anyone out of fear that someone may steal it. He also didn't want to lose one of the memories of his father. Kevin Flynn had built this "Grid" and made a clone of himself that helped with the construction. However, the clone went rogue, and Kevin was forced to sacrifice himself in order to save Sam. Sam hears a door open, and looks up to see Alan Bradley. Bradley is a friend of Sam who worked with Kevin Flynn at ENCOM before. "They're arguing, Sam.", says Bradley, "He doesn't like you here." "Tell him to come here.", says Sam tiredly. Bradley goes into the hallway and summons someone to come. A guy with heavy facial hair and glasses walks up and heads into Sam's office. This man was Edward Dillinger Jr. He was the son of Edward Dillinger Sr, who tried to steal Encom from Kevin Flynn. "Ed.", says Sam, "What is it?" "I am tired of your antics, Flynn!", says Dillinger angrily, "Think about the profits we could make!" Dillinger was very critical of Sam, as he wanted to make the consumer pay for new ENCOM software. "You know what my answer is.", says Sam, "I am not going to make the consumer pay for something that is required for their device." Dillinger glares at Sam. "If you aren't going to fix things, then I'm leaving!", he says, "In fact, I'll start my own company just so I can ruin yours!" He storms off, and slams the door behind him. Sam sighs heavily. He didn't enjoy sitting all day. He wanted to be active. A few hours later, and it is time for him to get off of work. He enters his car and plows through endless traffic. Rain bounces off of his windshield. When he finally makes it home, it is really late. He enters his home and sees Quora sitting in a chair, reading a book "Hey honey.", says Sam. Quora came from the grid and was brought along after Sam's father had sacrificed himself. She was an ISO. She wasn't created by Flynn, she was created by the grid itself. She was still adjusting to the real world. Sam walks up to her and kisses her on the cheek. As he walks away, she glances at the necklace around his neck. Sam gets in the bed, tired from all that he did at work. He falls asleep, but Quora is still reading in the den. After she notices that he is asleep, she sneaks into the room where he is sleeping. She sneakily lifts the necklace from Sam's neck and heads outside. She grabs Sam's motorcycle, and speeds off into the night. Sam then awakes in the middle of the night. He heads into the den and notices that Quora is gone. He then looks down at his chest. The Grid was gone. He heads outside and grabs the car. He had to retrieve that microchip.      

Quora speeds down the highway. She glances behind her as she rides, making sure no one is following her. She arrives at an abandoned arcade. At the top, old faded letters read: Flynn's Arcade. She heads inside where multiple arcade machines extend up to the walls. Yellowing tarps hand over each machine. She walks over to a particular one that doesn't have a tarp on it. The machine reads: TRON Light Cycles. She grabs the machine, and pulls it towards her, revealing a secret entrance. She walks down the stairs and through two doors. She ends up in an office where a touch screen computer sits in the middle. Dust is all over it. She blows it off, and inserts the microchip into a slot on the computer's disc drive. A message appears on the screen: Storage microchip detected, please initiate setup process for use. Quora appears desperate. She hastily activates the grid, ignoring the message, and turns on a laser that sits near the back wall. However, she accidentally hits a button that says create a program. But she doesn't notice. The laser shoots a beam of light at the computer, and Quora steps in front of it. She is split into many different pieces and enters the grid. She steps out of the grid version of Flynn's arcade and smiles. Meanwhile, the program that Quora accidentally created has glitched out. His conscience floats within the grid and comes into contact with a yellow circuit code. This code was the remains of CLU, the clone program that Kevin had created. The code is his feelings: anger, revenge, curiosity. The conscience of the new program is latched onto by CLU's code, and this creates a terrible force. The new program glitches into the grid, his torso, legs, head and arms lined with white and yellow code. He looks towards the grid city in anger, and glitches away. In the real world, Sam has reached Flynn's arcade. It was the only place that the grid could be activated at. He heads through the secret passage and finds the office. Just as he enters the office, Quora appears via the laser. "Quora?", asks Sam questionly, "Why have you done this?" She turns around in the chair and looks at sam solemnly. "I missed the grid...", she starts, "It felt as if something was drawing me there." "You could have said something.", says Sam. "But would you have listened?", says Quora, "You see I-" Suddenly, a blue glow fills the room. "What is that?", asks Sam. He walks over and suddenly, the laser comes on and teleports them into the grid. Sam looks around. It had been ages since he had been in here. He then feels droplets falling on his hands. He looks up and sees that artificial rain is falling from the sky. They head over to a nearby grid city and gasp at what they see: programs were walking around as if the grid shutdown had never happened. Billboards and advertisements hung from buildings. The grid was progressing. 

Sam looks at Quora in disbelief. He thought that the grid was shut down, erased. But the programs had been building and progressing the whole time that the microchip was around his neck. Quora opens her mouth to speak, but then is cut off by the sound of electricity. "You!", says a voice. Sam looks over to see a glitched program. "What do you want?", he asks. "Perfection. Rulership. Power.", says the program, "For you see, I am Ares!" Sam and Quora run into the city as Ares chases them on a white light cycle. They hide in an armoury closet and grab two light cycle disks that hang on the wall. Sam then realizes that his identity disc had been given back to him after he entered the grid. Quora's had been too. They run out of the armoury and jump. A motorcycle forms around both of them and they speed after Ares. Ares smiles beneath his helmet and gets out his identity disc. Sam and Quora speed around Ares and surround him from both sides. He collides with Sam's light trail, but disregards it and jumps onto Sam. He tries to crash him into a wall, but Sam deactivates his light cycle in time. Ares glares at them, but then laughs. "It matters not that you have survived.", he says, "My plan is already complete." He holds up Sam's identity disc which he swiped during the light cycle fight. He puts the disc on his back slot and his eyes glow yellow. He raises his hands and tears a hole in the grid, as if he were tearing paper. He steps through and vanishes. Sam grabs his light cycle stick and speeds into the tear with Quora and they end up in the middle of traffic. Cars dodge as they speed through and people grab their phones to record. Ares laughs from down below, and reveals the laser from Flynn's arcade. He had created a portal in the grid after he was glitched into existence, and stole the device. Sam and Quora head towards Ares and Quora uses her grapple to get them to the top of Encom Tower. "You are too late user!", exclaims Ares, "Soon my laser will bring this world into the Grid!" "I can't let you do that.", says Sam. He steps back, and Quora uses her grapple to get his identity disc from Ares. Ares pulls out his own disc and they have a disc battle. Midway into the battle, Quora collapses and Sam is in shock. "Quora!", yells Sam, "Come on, wake up!" He shakes her but she does not wake. "You have failed User.", says Ares, "Soon Clu and Ares will rule the Grid and the World!" "Clu?", asks Sam in shock. Then it struck him. Clu's memory was still in the Grid's files. Sam prepares to fight, but he is too weak from Quora's "death". Ares holds up his disk but before he can strike Sam down, he is pierced from the back by an unknown figure. Ares stands in shock and falls from the skyscraper onto the ground below. As he hits the ground, he turns into tiny little cubes. Sam looks up and sees the face of Alan Bradley. "Alan?", he asks. "You know my creator?", asks the figure. "Creator?", asks Sam. He then realizes that he isn't facing Alan Bradley, he is facing Tron. "You're alive?", asks Sam in disbelief. "Yes.", says Tron, "And you can thank yourself for that." Sam is at a loss for words but then looks down at Quora. "Do you know what happened to her?", asks Sam. "Yes.", says Tron, "A program or iso cannot last more than 8 and a half years in the real world." Sam gasps in shock. "So she isn't dead?", he asks. "Yes.", responds Tron, "We must take her back to the Grid." They lift her body and head into the grid using the laser. Sam lays Quora on the ground once they make it into the Grid. A blue glow emmits from her body, and she wakes up. "Quora!", says Sam. "Oh, Sam.", she says, "I didn't want to worry you. I tried to tell you, but we kept getting interrupted..." "Well I'm sorry.", says Sam, "I had no idea that the real world was killing you." "I'm going to stay here with Tron.", responds Quora, "I'll help him protect this world." "Good.", says Tron, "I'll need all the help I can get." Sam says his final goodbye, and leaves through one of Ares' tears. He looks on solemnly as the tear plugs itself back up. Sam walks away as rain falls on his head and shoulders.