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A shadowy program runs from his spot on a rooftop and jumps down. Upon pressing a button, he begins rewriting the code of Argon Square to say "Tron Lives". As the program finishes, Red Guards close in and chase him. The program disappears, much to the chagrin of the guards. Thinking the program to be the renegade, the guard corners the program, who turns to reveal a mischievous face on his helmet. Two other programs with similar circuitry, electrocute the guard and the three run away.
In Tron's hideout, he and Beck watch a security feed of the guards removing the gang's vandalism. Beck wants to bring the graffiti artists to the hideout because they are on the renegade's side, but Tron refuses. Tron says that Beck must show them what it means to join the revolution.
Paige lands her light chopper and takes command. She finds a package which when opened releases a countdown. She dives away, believing it to be a bomb, but it explodes in color and reprograms the circuitry nearby to say "Tron Lives". The three graffiti artists watching from nearby run away, happy that their plan worked. They make a clean getaway until a program with orange circuitry steps out and throws a bomb towards them that traps them in an orb. The program approaches them and tells them that they could be in big trouble for spreading propaganda.
Upon their confessing that they believe Tron still lives, Beck reveals himself to them as Tron. He asks them to remove their helmets so he can trust them. Moog and Rasket reveal themselves, and finally the third member, a female program, reveals herself to be Mara, much to the shock of Beck. Beck commissions the three to join him for a mission, to prove their loyalty. He tells them to meet again there at the beginning of the next cycle.
Getting Tron's advice, Beck questions his mentor about whether he was really Tron's first choice. Tron claims Beck was the first and that he chose Beck so that he could lead him down the right direction.
Beck tells the three vandals of his plan to board General Tesler's ship. Moog and Rasket believe they will be "hitting the ship" but Beck reveals his plan to have them draw the guards away to give the renegade a less covered area to enter the ship. Mara motivates the two to join in despite their doubts and the plan is set into motion.
As the ship draws nearer to the refueling station, graffiti pops up and the guards thin out. Beck takes advantage of the distraction and moves in but Moog and Rasket compromise the plan by going towards the ship instead of to the rendezvous. Beck stealthily enters as the two other programs crawl through the ducts. They begin to rewrite the code of the ship. Beck meets Mara alone at the meet-up location, and must re-enter the ship to rescue them. Beck tries to go solo, but Mara refuses to let him go alone.
In his throne room, Paige tells Tesler that the renegade has not been spotted. Pavel, however, points out the rewriting of the circuitry in the town and mentions that it is from their own ship's broadcasting. The two almost escape but upon cutting through the ducts, they are surrounded by guards and Pavel.
Pavel expresses his disappointment that they are not the renegade but he claims he will "still have fun" with them. He places the dissenters in two seats that will drain the energy out of them. Pavel questions them about their leader, the renegade. As he tortures them, Mara and Tron knock over the machine that sucks the energy. They rescue their friends as alarms begin blaring. Paige cuts them off, along with her red guard forces, and Beck fights them off. Moog and Rasket try to escape claiming "Tron" can fight for himself. A Recognizer appears in front of them and the pair flee, but Mara is braver and blasts color to rewrite the Recognizer. It loses control and knocks over a line of Recognizers, including the one Paige and Beck are fighting on. Beck narrowly escapes in his light jet, while the graffiti artists run away.
Moog and Rasket apologize for deviating from the plan and they realize that what the renegade is fighting for is more than just Argon City. Beck says he would like their help, but the male programs say they are not Tron's army. Mara however refuses to back down; she wants to aid Tron more. He tells her that she is not of any help because she lacks her friends now.
Beck meets up with Tron in Argon Square to tell him that this was the only way to get her to leave. Tron agrees that if she is really willing to help in the fight against the oppressors, she will keep fighting however she will. The next shot reveals Mara in a white hood admiring her new piece of art that says "Tron Lives".