Tron 2.0 came out in 2003 when Steve Lisburger wanted to do something to commemorate the 20th anniversary of the film. Disney was not interested in making another movie at that time, but did give Lisburger a small budget and permission to make a video game. In hindsight, this game turned out to be a test-run for TRON: Legacy and some of its related products like TRON: Uprising and TRON: Evolution.
The plot of 2.0 itself is that a rival company called Future Control Industries (F-Con) is looking to buy out Encom for the digitizing tech. They plan to use it to digitize groups of elite mercenaries into Datawraiths so that F-Con can obtain and control anything from credit card numbers to state secrets. Those who control the data, control the world. (The F-con CEO is never seen, but Word of God says it was Dillinger Sr. Of course, if you play Patchwork Fic and piggy-back this to events in Legacy's "The Next Day" bonus feature, it also could be Master Control 2.0.)
As far as F-Con knows, the only obstacle is Alan Bradley, who has been working obsessively on the digitizing algorithms since his wife's untimely death and close friend's disappearance several years earlier. (Yes, this came out well before Legacy. No, Flynn doesn't leave a pager behind in this timeline) He's hidden the data somewhere, but no one but him knows where. F-Con has been trying to work on the same technology on their own, but they haven't perfected it. Digitize a human without the proper corrections, and the end result is a virus-infected monster. They digitized the traitorous J. D. Thorne into the system, and he's become an unstoppable living virus with the powers of a deity, infecting Programs by the score.
The virus infected Programs go insane, and become Z-lots, fanatically loyal to Master User Thorne. While the Z-lots are infesting Encom's systems, F-Con pays an unfriendly visit to Alan Bradley to kidnap him so he can be intimidated into handing over the digitizing tech. An unsuspecting Alan is on the phone to his son, Jet. Jet hears the struggle, races downstairs, and Ma3a turns the laser on him.
Once in the system, there isn't much for characterization. Jet's aided by a Byte sent by Ma3a. Byte is very sarcastic and fairly oblivious to danger, while Jet is in over his head and just wants to find either Ma3a(to get home) or his dad (to help out). Worse, the Z-lots focus on him as a powerful Program to assimilate and the ICP (Infiltration Countermeasure Programs) think he caused the corruption!
Jet fights his way through several levels, and is able to free Ma3a from her docking clamps, but is eventually arrested and taken before the Kernel. A mysterious Program (later revealed to be Mercury) talks him into putting Jet on the Game Grid. Queue three rounds of Nintendo Hard lightcycle races. Mercury is current champion of the Games, and she uses a Flynn-style trick of making an escape route (in her case, a ramp of fallen debris to go over the wall). Jet dodges his opponents and vaults over the wall.
Mercury is a sultry, aggressive Program, and only knows her User as someone named Guest. ("Guest" is Alan, using the leftover computer parts, power outlet, and phone jack in his makeshift prison with a forged login - remember, this is Tron's User we're talking about. Locking him up with a bunch of old computer parts was the stupidest thing his captors could have done) She teaches Jet how to turn his lightcycle rod into an improvised weapon. Jet and Mercury split up to try and find Ma3a. Que more fighting until the Kernel declares the system a loss and engages a reformat. Jet is able to find Ma3a and head for an escape, but Mercury is caught in the reformat.
Jet is taken to Alan's home computer. Ma3a finally explains what the heck she was thinking when she zapped Jet a User would be the best chance of clearing the corruption from the system. She also suspects something in the Tron Legacy code (no relation, but worth a chuckle) will be able to help. Lucky for Jet, Alan is an archive nut. What else do you expect from a guy who probably still uses an abacus to balance his checkbook? There are three emails on Alan's system regarding a certain security program we all adore. Thing is, Alan had an upgrade almost ready, albeit one with a few bugs. Curiously, as he was about to apply that upgrade, the project was suspended....Flynn's orders. (Y'all went the same place I did, didn't you?)
Jet leaves and gets on a packet transport back to the Encom system. In the 2.0 universe, Recognizers (at least the obsolete models) have been re-purposed into mass transit. He goes through the power routing system to get the archaic 1982 server back online (lots of brawling and jumping, not much plot), and then it's out of frying pan and into the fire with a Seeker. Think those sandworms from Dune colored a sick pink-purple and shooting lasers from their orifice.
Well, he takes out that and gets dropped into the ancient mainframe. Here's where life gets interesting. The Tower Guardian, I-No, is an extremely pleasant guy. He also lets it slip that he was one of the Guardians the MCP kidnapped at the end of the first film. He curiously mentions that while the legacy code is on the server, Tron himself retired, then vanished from the Encom servers shortly after Master Control's defeat. No one knows where he is or what became of him. Thing is, there are also a gauntlet of tanks to run, which Flynn programmed to be indestructible and read-only (Flynn, you idiot!). So Jet runs the gauntlet, heads into the heart of the server, and has to overclock the thing so Ma3a can be uploaded to safety. The predictable results occur of the system shaking itself apart. However, he does reach Ma3a, I-no and the Legacy Code (which looks like a golden sphere). Jet gets the code, and escapes with Ma3a, but the old Guardian chooses to stay with his system to the end.
Next stop is the internet, which looks like a bustling city - neon lights, lots of traffic. Jet and Ma3a need a compiler to help them with the Legacy Code. They find one, but he isn't strong enough. And it seems that every Program around has heard of Tron. His conspicuous absence is also a topic of speculation, the great hero with an unknown fate, prophesied to come back in the system's Darkest Hour. The low-level compiler recommends heading to the Progress Bar. Unfortunately, there's an onslaught of Z-lots and Jet has to hold them off. After the fight, he meets Mercury, but she doesn't know who he is and her personality is gone. She's been re-installed from backup. After Jet fights off more Z-lots and a Rector Script (think a wraith or mini-Abraxas that spews the virus, infecting Programs in range), a grateful citizen gives him the permission to enter the Progress Bar.
The Progress Bar is a cousin of the End of Line; a place for the Programs to relax, dance, have a drink of energy, and hang out. There's also a compiler for those who want to use it. The DJ...well, he's no Daft Punk. So, Jet asks around and finds a tune most of the Programs would like played. While everyone's on the dance floor, he gets the code compiled. The code itself goes into Ma3a. (However, Jet also volunteered to be a host for it! If that's not Fanfic Fuel...) The corrupted Thorne shows up and Jet has to hold him off while Ma3a is compiling the Tron Legacy code into her system. Worse, No sooner has that code compiled than Jet gets a video message from Alan warning him not to do it! Remember that bug from earlier? Yeah, Alan never worked it out.
The bad code causes Ma3a to go insane, killing Byte in the process. Jet hops on his light cycle and runs for his life. Just as he's managed and escape, a Seeker grabs Ma3a. Jet fights his way across a remote node with the help of the amnesiac Mercury to get to Thorne's secure server and unlock the door to Alan's makeshift prison.
Back at the F-Con labs, it's explained that Alan hid the algorithms for the digitizer in Ma3a, explaining why Jet suffered no ill effects from the digitization. F-Con sent the Seeker to appropriate her for the Datawraith project. An Encom employee (they're merging the companies) also expresses worry that several Encom employees, including Thorne and the Bradleys, have gone missing. The F-Con guy ignores the Encom one. Worse, Alan gets caught outside the storeroom. Crown, the nastiest of the three F-Con goons, decide to make an example/test of him and throw Alan in front of the digitizer, zapping him into the system. (This was probably F-Con's second-dumbest move.) After they verify Alan is still alive and reasonably intact after zapping him, they prep the first batch.
Jet finally gets in direct contact with Alan, but Alan looks different. In fact, he looks like he borrowed his old security Program's duds and looks ridiculous in them. See for yourself. They're both on Thorne's server a Sickly Green Glow apocalypse. So while Alan hides from corrupted Programs (he's unarmed), Jet sides with the ICP Programs to fight off the virus. They'll need to find one another and then find Ma3a, as she had the algorithms to get them home. Thorne knows how to get to the F-Con servers and where they'd hide Ma3a, so they need to find him before the ICP units do. Eventually, Jet battles his way up to the system's core. Thorne's there, Alan's there, but so is the ICP Kernel, and the Kernel just wants to de-rez Thorne and Jet outright! However, the Kernel allows a one-on-one battle with disks to determine the winner. Jet dispatches the Kernel, but Thorne is on the verge of death. Before the poor bastard finally dies, he tells the Bradleys that his PDA has a dial-up connection that bypasses the firewall.
Jet gets uploaded to the PDA, but the PDA is junk; Alan has to be left behind. From inside Thorne's PDA, Jet has to turn everything on and put such a drain on the memory and power that the OS decides to cry uncle and push him to the F-Con server. All well and good, now all Jet has to do it bring Alan over. Brawling his way through F-Con's sockets, he finally knocks down enough of them to take down the firewall. Here is his first encounter with Datawraiths. They're neon purple, masked, and can appear and reappear at will. They also don't speak, instead emitting an eerie clattering noise that Rinzler would only make on his worst day. The Programs are terrified of them. Configuring and aligning the socket rings, the connection is made, and Alan's through! Cut to the F-Con lab where Crown, Popoff, and Baza are freaking out about not being able to locate Alan in the system and that there seems to beanother User inside the system helping him.
Jet clears the area of Datawraiths and F-Con ICP units for Alan to follow. They discover the virtual server F-Con plans on using to deploy the Datawraiths across the internet go steal information they oughtn't have. Alan takes a look at the schematics while Jet goes to take out the server's docking clamps. Jet heads to the tethers and Alan contacts him. The server is powerful, but unstable. They're going to crash it from the inside. Jet wonders if they'll go down with the ship. To Alan's credit, the idea of a Heroic Sacrifice never crosses his mind. The plan is to destabilize the server, grab Ma3a, and get out before it crashes. (Apparently, that dying heroically nonsense is Flynn's tactic, not Alan's!). Meanwhile, it seems that when Jet de-rezzes a Datawraith, the corresponding mercenary is dumped back at F-Con's digitizer lab, unconscious. They finally figure out that there really is another User in the system helping Alan out. And while the poor bastards at least survive long enough to get to a doctor, we have no idea whether or not they remain alive for long.
Jet takes out the docking clamps, fights off a squad of Datawraiths, then heads to the cargo bay. More Datawraiths and another Seeker wait. He takes those out and hops a transport to the server itself. Fighting his way down to the server's core, he starts engaging a series of override circuits until the server starts to take down functions to stay online. He then finds Ma3a and Alan, surrounded by ICP guards. Again, Jet dispatches those. Alan takes over trying to debug Ma3a while Jet heads to the stabilizers once those go down, the server is history. To do so, it's another lightcycle chase against Datawraiths in training and they consider five of them to one opponent perfectly valid odds. Just when it looks like Jet isn't going to be able to hold out, a fully-restored Mercury swoops in and helps Jet corral the Wraiths.
And that's when the Terrible Trio at F-Con decide they're going to win the Darwin Award and go in themselves! Baza balks, but Crown uses his usual combo of bribe and bully to get Baza in on this insane stunt. They get digitized...but Alan's freed Ma3a. The Terrible Trio became corrupted in transport.
Jet is able to get into the command module and start the system crash. Again with the horde of Datawraiths and IC Ps trying to stop him while the place is literally falling apart around his ears. Just as he reaches the digitizer stream to go home, he sees Mercury. She's sad to see him go, and comments that the Program world is too crude and rudimentary. Jet replies that humans are the crude ones, and that we're not ready to exist in the Program's world. He tells her to save herself, and she promises she will. Ma3a activates the beam and Alan steps inside. Unfortunately, when Jet does, the Terrible Trio are right behind him, fused into a three-headed twisted abomination.
On a series of floating platforms, he battles the creature eventually knocking each one off and into limbo. As the last one is defeated, the digitizer kicks in and he arrives, safe, at F-Con labs. He's a little shaken about the whole thing, and comments that he'll never drop another laptop again. Alan retrieved Ma3a and Mercury managed to escape the server. As for the Terrible Trio? They're on a ultra-secure external hard disk, and Alan will try to do what he can for them...but it seems he's not in a big hurry to do so. F-Con's mysterious overseer threatens revenge, but Alan cuts the speakers in mid-threat, saying he'll deal with that later, and the Bradleys walk out of the lab and away from the computers for a while.