In 1988, while inside the Tron system, Kevin Flynn bore witness to the arrival of the ISOs. This new breed of program had evolved within the system simply because the conditions existed for their evolution. Flynn saw their appearance as a "miracle". As far as Flynn was concerned, the Tron system had simply given birth to a new form of life.
Both the Tron and Clu programs were also present at the time, and while Tron simply looked on and followed his directives to ensure security, Clu's perspective as a system controller had an altogether different impact. Clu's directives drove him to create the perfect system and yet to him, the ISOs represented an element of chaos - a taint that must be eradicated to ensure that perfection be allowed to thrive.
Clu, realizing his position on the ISOs would contrast with Flynn's, bided his time while amassing a power base to launch a coup that would restore perfection to the Tron system. Finally, he launched his attack in 1989, inquiring of Flynn, "Am I still to create the perfect system?" Flynn's quizzical, affirmative reply fell on deaf ears as Clu and his Black Guards attacked, defeating both Tron and Flynn in the process. Flynn was forced into hiding and disappeared into the Outlands to escape the tyranny of his rebellious program.
With Flynn gone, there was nothing to prevent Clu from doing as he pleased within the Tron system. His forces set upon the ISOs with a ferocity never before seen in the Grid. Their purpose was simply to destroy every last ISO in the name of perfection. ISO dwellings were razed to the ground, and their citizens hunted down in the streets. No matter where they fled, Clu's forces would eventually route them out and destroy them.
The genocidal event later came to be known as "The Purge".