The story is centered around Alan's son Jethro ("Jet") Bradley. Since the film's events, ENCOM has been taken over by a company called Future Control Industries (fCon). After talking with his father who is kidnapped while on the phone with Jet, Jet is digitized by Ma3a, Alan's AI computer system, to aid her against Thorne, an executive from fCon improperly digitized into the computer who is now a virus throughout the system. Jet is mistakenly identified as the source of the corruption and captured by Kernel, the systems security control program.After deciding that Jet is corrupted, Kernel spares Jet on the recommendation of Mercury, another program tasked to help Ma3a, and Jet is sent to the lightcycles game program. After winning several matches, Jet escapes the match with Mercury's help. After they find Ma3a, the server, corrupted beyond saving, is reformatted resulting in Mercury's demise. Jet escapes to the Internet with Ma3a and an uncompiled copy of Tron Legacy, an update of the original 'Tron' program written by Alan Bradley to protect Ma3a. After finding a compiling program on the Internet, Thorne appears to kill Ma3a while the Tron code is compiled and attached to her program. During this, Jet receives a communication from Guest, the User who had assigned Mercury to help Jet. Accessing a video uplink, Jet realizes too late that Guest is his father Alan, locked in a storage closet by fCon's officers Bazra, Popoff and Crowne, begging him not to compile the Legacy program. Legacy activates, revealing that its sole function is to kill any User in the digital world. Jet escapes, and fCon inadvertently saves him by capturing Ma3a in a search programHaving recovered the correction algorithms necessary to digitize a human, Alan is sent to Thorne's corrupted server. Assisting the ICPs and Kernel, Jet reaches Thorne at the heart of the server and kills Kernel before he can destroy Thorne. Thorne, regaining a moment of lucidity, begs for forgiveness and tells Jet how to enter fCon's server.