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Scars, Part 1
Pavel, Paige, and Tesler greet Dyson on the command ship. Tesler is unhappy to see his superior, who is only there to review Tesler's work as well as the renegade problem. Tesler tasks his two commanders to make sure Dyson's visit is "short and uneventful." Tron and Beck watch on. Beck is unsure why Tron had to accompany him but Tron maintains that his plan is for Beck to capture Dyson and bring him back the hideout. Beck thinks the plan is unsafe but agrees to it.
In a flashback, Tron and Dyson work together as security programs, investigating problems in the ISO district with their teams. Because the programs want to remain separate from the ISOs they revolt. The security teams forms a line between the two groups to convince them to share the Grid with each other, until a disc is thrown and many ISOs are derezzed. Dyson takes a disc to the face.
Tron runs Beck through an insane simulation to prepare him to face and take down Dyson.
Pavel tries to convince Paige to join him, thinking that Tesler may be demoted by CLU.
In the flashback, Dyson, still showing the gash on his face, and Tyson wait for CLU 2.0 and Flynn to decide the fate of the ISOs. Flynn tries to convince Dyson that the ISOs are as much part of the Grid as normal programs.
Tron almost steps into the healing chamber but because of his hatred he steps back and his scar darkens. Beck plants a false bomb on Tron's disc. Tron throws it and Beck catches it saying "if you saw I could get your disc, you'd know I could get Dyson's." Tron scolds Beck saying he wants Dyson and if Beck pulls a stunt Tron will begin the revolution without Beck.
Beck plants a smoke bomb where Dyson will be walking but Dyson finds Beck's footprints and the bomb and tosses it into the air where it detonates. Paige, who had just been assuring Dyson the renegade was no problem, sed guards to search the area. Pavel suggests that the renegade might be Tron, but Dyson says he is assured Tron is dead because he saw Tron's death with his own eyes.
In the flashback, Dyson sets guards to derez Tron and Flynn because they stand in the way of CLU 2.0's plans.Tron heroically but sustains multiple slashes on his chest. Dyson steps out of the shadows to reveal a perfect face, free of his scar. CLU cuts across Tron's face and leaves him for dead.
Beck returns and confronts Tron about his intentions, but Tron shocks Beck, taking the Tron disc, and leaves.
Scars, Part 2
Beck regains consciousness on the floor and takes off after Trom. As the two race through the Outlands, Beck tries to convince Tron that what he is doing is wrong. Beck and Tron remain neck and neck but Beck gives in as they approach a pile of junk, where Tron grabs a pole that disables Beck's bike. He jumps a ravine but is unaware that Beck placed a tracker on his bike.
Tesler is not happy to hear of Dyson's close call with the renegade, but Dyson "senses a lack of control" with Tesler's command and threatens to potentially take over permanently. Paige guides Dyson on his tour but she must investigate the cause of a coolant overload.
In the flashback, Tron wakes up in a repurposing chamber where he watches the repurposing of Reeve, a member of his security team. Dyson brings him up to a room where Tron is restrained.
Tron is surprised that Beck found him but refuses to be stopped. The two fight and Tron steals Becks disc and handcuffs him to a rail with time-release handcuffs that will unlock after his plan has time to be finished and Dyson is dead. Tron lodges Beck's disc in a wall.
Paige discovers that it is Pavel who attempted to cause the overload while Beck reaches to obtain his disc and Dyson seeks out "the renegade." He charges at what he thinks is the Tron emblem but it turns out to be a series of bombs which explode.
Again in flashback, Dyson personally fixes some of Tron's wounds. A guard outside the door questions why the person being altered is not screaming as others typically do and the other guard replies "He's Tron." Tron is informed that he is Flynn's last soldier. Because Tron will not join CLU willingly, Dyson uses a cutting tool to mar Tron's face and has him taken to the throne ship. An explosion occurs in the Recognizer carrying him and the Recognizer goes down.
Tron confronts and fights Dyson but Beck is still frantically reaching for his disc. Dyson knocks down the renegade and tells him to remove his helmet so he can look on his face before derezzing him. Escaping the pin down, Tron fights intensely and finally grabs Dyson's disc. Beck also manages to free his disc from the wall and catch it. As he goes to stop Tron, he must clear a gap. Tron removes his helmet and corners Dyson. Beck hardly clears the gap. Tron, holding Dyson by the neck, contemplates his fate.
In the flashback, Tron is saved by Cyrus, one of the guards and the two escape the Recognizer. Beck says the reason he saved Tron was because "You can't let a revolution end before it has a chance to start."
Tron drops Dyson and tells him to deliver a message to CLU. Beck watches on, proud of his teacher. Tesler is happy with Dyson's departure.
After some time in the healing chamber, Tron thanks Beck and apologizes to him for taking his eyes off the big picture and focusing on revenge.
Dyson returns to CLU to tell him that "Tron lives." CLU asks who knows about this, and after Dyson derezzes the guard and informs him that no one else knows, CLU says to keep it that way.