After finding a compiling program on the Internet, Thorne appears to kill Ma3a , who Jet fends off while the Tron Legacy 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 Baza, Popoff and Crowne, begging him not to compile the Legacy program. Legacy activates, revealing that its sole function is to kill any rogue User in the digital world. Jet escapes in a lightcycle, and fCON inadvertently saves him by capturing Ma3a in a Seeker search program.
Having 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 as he dissipates.
Alan and Jet break into fCON's server, which the corporation is planning to use to distribute Datawraiths - digitized human hackers - across the worldwide information network for plans of corporate and international espionage. After Alan and Jet crash the server, the CEO of fCON (possibly Dillinger of the original film, though this is never confirmed) orders Baza, Popoff, and Crowne into the system themselves. Alan, wanting to verify the purity of the correction algorithms, removes them from Ma3a to inspect them as the three are digitized, resulting in a monstrous amalgam of the three, which chases Jet into the digitizing beam. Jet diverts the three out of the beam and escapes the computer after battling the digitized monster, releasing their code from the corruption one by one. Severing off the CEO's control, Alan and Jet extract and save the Legacy code as the ENCOM servers crash, with Alan planning to reassemble the fCON team as before un-digitizing them.
Gameplay
The single-player campaign takes place entirely inside the computer's world (though some cutscenes are shown of the ENCOM research laboratory). The goal of each level is generally to complete tasks and find keys ("permission bits") which allow access to the next level.
The design of the game's levels is linear; there are no choices about how to proceed or of what to say during the interactions with other characters. The levels feature energy bridges and gates, neon-glowing contours, vibrant colors, floating boxes and tiles, teleports and deep chasms. Jet will be harmed if he falls from a height (or killed if the height is great enough), or be crushed by certain moving objects in the digital world.
Jet begins with the disc weapon seen in the movie; but obtains other weapons similar to a shotgun, a submachine gun, a sniper rifle, and grenades. Ammunition for these new weapons is energy, which Jet can collect at various points during the game (an exception is the disc, which uses no energy in its basic form). The in-game names for these weapons are, respectively, disk, rod, mesh, and ball. The other weapons are upgrades of these basic weapons (called "primitives").
Jet's abilities are customizable, as his in-computer program earns "build counter" upgrades - when earning a level, Jet 0.0.0 becomes Jet 0.0.1, and so on. He acquires new abilities, and also the aforementioned weapons, in the form of "subroutines" held in "archive bins" scattered around the levels, and he has a limited number of memory slots in which to "install" these subroutines onto his person. Subroutines start out as alpha-grade software, but can be upgraded to beta and gold statuses, which both take up less space in memory and become more effective.
As he moves through the levels, Jet must engage many lower-tier enemies. Although none are particularly powerful, they usually appear in gangs, making them more of a threat. Among the regular levels, there are some with boss enemies.
Interspersed with the first-person-shooter levels are several light cycle races. As seen in the movie, these races are actually arena duels in which each light cycle attempts to destroy its opponents by driving them into its jetwall. The arenas contain 'improvements' (such as speed zones that affect the cycles' speed), more complex layouts with walls and other artifacts (instead of the "empty box" as seen in the movie), and power-ups that can be collected during races. In addition to Tron's regular light cycle, Jet can also gain access to the super light cycle that sports a more modern design and offers more speed. Tron 2.0 initially required the player to win the light cycle races in order to advance the campaign. Consumer feedback revealed that many felt the computer-controlled light cyclers were impossibly precise in their controls (turning at speeds a human could not, or boxing themselves in,for example), forcing players to wait for the enemy light cycles to destroy themselves. As a result, the vendor released a patch eliminating this rule.
The additional light cycle mode contains no campaign; instead, the player is presented with a choice of several light cycle arenas.