Tron sends Beck out on a mission to sneak into one of Tesler's bases in order to retrieve a data cube. He uses his stealth skills to locate the cube. Paige sits in her room reminiscing in an old memory until an alarm goes off. Pavel and Tesler watch as the renegade begins fleeing and the general dispatches Pavel to stop him. Beck narrowly slips through a closing portal on a light jet with Paige in pursuit on a light chopper and others following in jets. They all begin firing at him. Beck evades the jets but Paige hones in on him and fires on him as he leaves a streaming Light Ribbon, which causes her to spiral downward. Having been hit, Beck also descends. Beck is stranded on an island when his jet collides and explodes. Pavel looks upon the wreckage with glee, thinking that the renegade is no more. He passes over Paige on the same island but refuses to pick her up.
In a flashback, it is shown that Paige was trying to become a medic although she was programmed for music. She witnesses three male programs menacingly approaching two female programs (one of which was Quorra). She uses her disc to fight off two men as Quorra throws the third. Paige helps heal the wounds of the other girl. Quorra informs the three medics that the two girls are refugees leaving their town which was destroyed because of ISO's.
Beck sees that the world is practically caving in around him. Nearby, Paige is tearing her ship apart in hopes of fixing it. Beck calls out to her but she tries to derez him. He tries to inform her of the imminent danger but she proceeds to fight him. The data cube flies from Beck and Paige snatches it up before he can and runs away. Paige ends up clinging to a cliff because of tremors. He saves her from her dangerous position because she agrees to stop fighting him. She tells him that she intends to make her chopper float since it will never fly again. She launches a piece of debris into the water but as the piece loses power it breaks apart and Paige sinks into the energy sea. She swims back to shore and almost falls through a large hole as the island crumbles. After much deliberation and convincing, she finally agrees to cooperate with the renegade. She sees a wound on his arm and says she can heal it if she can access his disc. The two form a truce and Beck hands the disc over. She quickly heals his wounded arm.
In the flashback again, Paige shows the refugees her expert music ability. Quorra teaches Paige some of her fighting techniques but Paige realizes that Quorra is an ISO when her symbol shows from under her sleeve. Paige is about to press a button to alert the authorities but Quorra talks her into helping them. Rox tries to get to the bottom of the refugees' situation but Paige refuses to tell her. Quorra knocks down Paige after Recognizers fly in to find the ISO contaminants in the city.
Waking from her sleep, Paige finds that the renegade has constructed a boat. Paige relinquishes a power pack to power their boat but the ground falls out from beneath her.
Again in a flashback, two guards pick Paige up off of the floor but Paige beats both off using moves that Quorra showed her. One guard is revealed to be Tesler who tells her that the rest of the programs in the building were derezzed by the ISOs. She joins his army, with an intention to get back at the ISOs.
Clinging to the edge, she feels that Beck has abandoned her but he is actually powering up the boat to catch her. Tesler flies in with a chopper to retrieve his second-in-command but she falls into the sea. Beck dives in to save her, until a claw from the chopper grabs her out.
Beck makes it back to Tron, sad to inform him that he failed to retrieve the data cube. Tron tells Beck he respects him for aiding an enemy.
Tesler expresses distaste that the renegade got away but is proud of her nonetheless. In the final flashback, it is revealed that Paige's friends were the ones who informed Tesler of the ISO presence, but he betrays them by having them derezzed for even knowing the ISOs. He tells her that he would never betray her.