Clu 1 was developed by Kevin Flynn to hack into the the ENCOM computer system in order to expose an ENCOM programmer who stole Kevin Flynn's video game idea, leading to Flynn getting fired. While Clu was hacking into ENCOM's computer system, he was discovered by "Recognizers" and was derezzed by the Master Control Program shortly after.
Clu 2 was made for the single purpose of creating and maintaining the "perfect system". During this time, new programs called Isomorphic Algorithms (ISOs) started appearing in the Grid. It was revealed that they were evolved programs who self-created without users. Because of their unpredictability and imprecise function, Clu 2 saw them as imperfections and a threat to the Grid's stability, although Kevin Flynn saw them as "miracles". Because Flynn remained absent most of the time, Clu 2 was unable to get his approval and was left with no directive. Clu 2 soon realized (in his own mind) that since he was created by Flynn to be like him, he was the true creator of the Grid and conspired against Flynn. Clu 2 began his new order by taking action against the ISOs. He was against evolution in the Grid and believed the ISOs to be imperfections that were damaging the Grid and causing glitches. Because of this Clu 2 created the "Abraxas virus". This was meant to degrade and eliminate the ISOs by infecting one of their leaders, Jalen. After a failed attempt to use Jalen (Abraxas) to convince Flynn that they were a danger to the system, Clu 2 decided to kill his user. Clu 2, with the assistance of four Black Guards, ambushed Tron and Flynn. While Clu 2 focused his attention on Flynn, telling him he's been "corrupted" Tron was left to fend against of guards. After easily defeating them, Tron attacked Clu 2, telling Flynn to go. Although Clu 2 got the better of Tron (knocking him down and directly hitting him with his identity disc), Flynn escaped. Clu 2 then focused his attention on the ISOs. He created a genocide which would later be known as "the purge". Clu 2 was successful in eliminating all ISOs except for Quorra.
With Tron gone, Clu 2 began his rule over the Grid by sending his armies to control every city. This resulted in the appearance of the renegade program Beck, who was going under the disguise of Tron. Unknown to Clu 2, Tron had actually survived and was training Beck in secret. Although, Clu 2 still concluded Tron was dead.
During the events of Tron: Legacy, Clu 2 had taken complete control of the Grid, fashioning it into his own image of the perfect system. However, he felt this wasn't enough. He realized true perfection remained beyond his reach, in the real world. He sought out to acquire Kevin Flynn's identity disc in order to use the portal to invade the real world and create a perfect world outside of the Grid. He sent a message to Alan Bradley (Tron's user) in hopes of luring a new user into the system. This was successful when he found out Kevin Flynn's son, Sam had entered the system and was defeated by Rinzler in the disc wars. He then planned his own form of execution by defeating Sam in a light cycle battle, but was interrupted by the last ISO, Quorra, who rescued Sam. Clu 2 then eagerly awaited Flynn to make his turn. After finding Flynn's deserted safe-house, Clu sent his forces to the End of Line club where Castor was keeping Sam. The battle seemed hopeless until Kevin Flynn entered. His very presence caused the programs in the club to turn on Clu 2's soldiers. Although they escaped, Flynn's identity disc was captured. After acquiring the disc, Clu 2 prepared his army for the invasion. With Clu 2 being distracted, Sam and Quorra successfully took Kevin's disc back. They attempted to escape using one of Clu 2's light jets, but were eventually overwhelmed by their persuers. Clu 2 was almost successful in acquiring the disc had it not been for Rinzler's (Tron's) sudden betrayal. Clu 2 confronted Kevin, Sam, and Quorra at the portal, pleading that he had done everything Flynn told him to do, but was told by Flynn that he wasn't able to acquire true perfection because Flynn didn't know what perfection was at the time when he created Clu 2. Clu 2 then attempted to persue Sam and Quorra to the portal, but was failed when Flynn reintegrated Clu 2 back into himself, resulting in his immediate de-resolution.
When he was first created by Kevin Flynn, Clu 2 worked alongside Flynn and Tron. Clu 2 inherited Flynn's appearance, ideology, as well his idea of perfection. Because Flynn had a flawed sense of perfection at the time, so did Clu 2. As the Grid progressed, Clu 2 began disagreeing with Flynn's methods and ideals. Where Flynn saw the ISOs as a "miracle", Clu 2 saw them as an imperfection. He later became cold and ruthless. During the final events of Tron: Legacy, Clu 2 pleaded that he did everything Flynn asked him to do and it was revealed that when Flynn left, Clu 2 felt betrayed and became jealous of the ISOs because Flynn turned his attention onto them.