[GoldenRivet]

Flynn created Clu to assist him in making the digital utopia during the times that he was absent.

A few things contradictory to clu's idea of perfection took place (things I won't go into here) and this left Clu feeling as if his direction to create the perfect system were no longer valid orders or perhaps that Flynn no longer desired to do this. Also I sensed that clu may have become jelouse of Flynn's god like status (and other things).

In the scene where Flynn is walking back to the portal with his friend to head back to the real world, clu shouted to Flynn from a distance.

Clu: "Flynn!!!!!"

Flynn: "yeah?"

Clu: "am I still to create the perfect system?"

Flynn: "yeah..."

Clu: "very well"

Clu removes his disk and tron appears from the shadows and removes his, fight ensues, ultimately leaving Flynn in exile, trapped with no way to open the now closed gate from inside.


EDIT:


also... Tron Legacy had an AWESOME soundtrack