Flynn reveals to Sam that he had been working to create a "perfect" computer system and had appointed Clu and Tron (a security program created by Bradley) its co-creators. During this construction, the trio discovered a species of naturally occurring "isomorphic algorithms" (ISOs) not conceived by Flynn, bearing the potential to resolve various mysteries in science, religion and medicine. Clu, considering them an aberration, betrayed Flynn, seemingly killed Tron, and destroyed the ISOs. Meanwhile, the "Portal" permitting travel between the two worlds had closed, leaving Flynn trapped in the system. Having gained complete control, Clu sent the message to Alan in order to lure Sam onto the Grid and reopen the Portal for a limited time. As Flynn's "identity disc" is the master key to the Grid and the only way to traverse the Portal, Clu expects Sam to bring Flynn to the Portal so he can take Flynn's disc, go through the Portal himself, and impose his idea of perfection on the human world.
Clu , which stands for Codified Likeness Utility , was a hacker program written by Kevin Flynn and played by Jeff Bridges . Clu looked just like his user, Flynn, but talked in a very different voice than his human counterpart. Not much is really known about Clu, except for the fact that Flynn used Clu a lot for hacking and for fixing Flynn's banking statements and phone bill problems. Even Flynn himself said that Clu was his best program .