CLU 2 is the main antagonist of Tron: Legacy and the secondary antagonist of Tron: Evolution and Tron: Uprising.

Even before the Great War was fought, mankind enjoyed a relatively golden age. At certain spots, technology flourished and grew, while at other spots, it was shunned and seen as unholy. Even so, one of the masters of technology, Kevin Flynn, managed to do something beyond the minds of his other men. As he was the proud owner of a arcade hall and managed that pretty well, he sought in secret to create the perfect world. A world without war, without hunger or thirst, and a world without any kind of violence. 

Flynn designed his world to the max. Instead of fights to settle conflicts, he organized games in which the programs dealt with their problems against another. These games were relatively harmless and were enjoyed by other programs to watch. To see to it that the system never lost its shine, Flynn designed two programs to keep watch over it. Tron would be the one to see no violence would ever escalate and Clu was designed to see to it that all rules would be lived up to a giant expected level. Flynn and Clu promised each other that the system would indeed be a perfect world.

Flynn's dreams were utterly destroyed when the Great War broke out and he lost control over the system forever. Now without their creator, the programs that were designed to hold peace and order kept up their level to the max. Clu and Tron worked tirelessly together to see all programs Flynn had designed would never fall out, and thus the darkness inside the system was kept to low levels.

Even as the world was split and torn asunder in the final act of the war, the system somewhow managed to stay intact as one giant world. Clu, however, did find out that now the once created portals that allowed programs to get in from all over the world suddenly were connected to different realms. As such, he saw imperfect programs from different realms instead of programs

CLU 2 as he appears in the CGI Universe

from just one world. Though Tron reminded Clu that there was no actual big change, Clu thought otherwise.

Frightened and terrified, Clu fell out with Tron, which saw the first conflict with violence in the system. Some say that on that day, Tron died and Rinzler was born from his ashes; a warrior designed with only one purpose: the destruction of all imperfect programs. The slaughter that then ensued was beyond counting. Clu fortified his position of a tyrant and dragged the system into a spiral of never-ending violence. New and imperfect programs that were created by the different realms were either derezzed or reformatted into soldiers. Clu saw to it that nothing escaped his attention.

As part of these changes, Clu included one last big change. Those imperfect programs that he saw as threats, he had captured and fight for their lives in lightcycle battles. These fights always ended with only one standing, and when Clu himself participated, it always meant he was the last one standing. 

He never encountered any kind of problem anymore... untill a master control program interfered with his life long work.

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