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|“||Clu. Clu happened. It was a coup.||”|
In 1988, Kevin Flynn discovered that, independently from him, the Grid created programs known as isomorphic algorithms (ISOs) who were capable of changing the Grid in ways unplanned by Flynn. He regarded that as a miracle and "a digital frontier to reshape the human condition". However, Clu was written, according to Flynn's earlier ideas, to strive for "the prefect system" and thus viewed the ISOs as sources of imperfection and chaos, and a threat to the system.
As unrest among the Basic programs grew due to clashes with the ISOs, Tron and his police force went to Tron City's ISO district to calm down the protests. What Tron assumed to be a provoker threw a disc that derezzed a Basic program, inciting violence. In the ensuing chaos, Tron's second-in-command, Dyson, was disfigured, causing him to hate the ISOs he already distrusted. A visit by Kevin Flynn made things even more bitter when the User neglected his Basic programs while showing excitement about the ISOs.
Flynn was met by Clu while discussing security issues with Tron. Clu sardonically asked his creator whether his directive was "still to create the perfect system", which excluded leaving any ISOs alive. At Flynn's wary "yeah", Clu activated his mask and ordered some Black Guards that were waiting in ambush to attack.
Tron covered Flynn's escape, engaging the Black Guards all by himself. He was quickly overpowered and finally brought down by Clu. Flynn only saw as much before he escaped, assuming Tron was dead, when in reality Clu enslaved him and turned him into his enforcer, Rinzler.
In one fell swoop, Clu disposed of the system's creator and monitor program, allowing him to execute his directive unchallenged. He subjected Tron's former team to repurposing. Then he went on to conquer every corner on the Grid via military occupation.
It was revealed that not only did Tron survive, but his enslavement didn't follow immediately after the coup. Instead, he was tortured and incapacitated by Clu's right-hand program, Dyson, as a revenge for Tron's inaction when Dyson, Tron's subordinate at the time, was disfigured as anti-ISO protests escalated. As Clu was giving a victorious speech before his newly repurposed soldiers to rally them for the Purge, Tron, half-derezzed, was hauled onto a recognizer that was supposed to take him to Clu's throne ship. However, a sentry named Cyrus, who had come to admire Tron for his stoicism, caused the ship to crash and escaped into the Outlands with the injured Tron to start a rebellion against Clu. Dyson, who only saw the recognizer explode, left Tron for dead.
- In TRON: Legacy, four Black Guards approach Flynn and Tron from each corner. Tron says "Go" to Flynn in a low voice and engages the guards. Clu attacks Flynn, telling him that he's been corrupted, before he's tackled by Tron. Tron yells "Flynn, go!" and then Clu overpowers him, jamming a disc into his chest, after which Rinzler's growl is heard, suggesting that Tron's repurposing happened at this point.
- In TRON: Evolution, Tron yells "Flynn, go!" as he is surrounded by the guards. Anon watches the scene from a higher level.
- In Tron: Uprising, the ambush is commanded by Dyson who's watching from Clu's right. On his order, at least ten black guards swarm the pair. Tron says the "Flynn, go" line in a low voice before attacking. Afterwards he's shown lying on the ground heavily wounded, with Clu gloating about having eliminated him and lured Dyson to his side. Tron is depicted wearing his white suit in this scene, unlike in the film and the game.