With the beginning of talks about Tron 3, I started to think about possible theory's about the sequence of the movie or the story line. I was thinking, What if the clone of Kevin Flynn, Clu, was not actually destroyed or brought down 100%.
At the end of Tron: Legacy we see Sam take a upload of the game to his phone or electronic device and make a SD card copy of it or something like it. Then hangs it around his neck. What if that since the meaning of Clu is Codified Likeness Utility or a hacker program made by Kevin so he could create the "perfect" system. Since Clu is a hacked program or a hacking program, would that mean that he could have imprinted in the system a copy of himself or something like him so if he failed that the dream he had would live on. With Sam making a copy of the game or user profile, that would carry the Clu copy with it. If Sam were to plug the system back in and start the game, that would make Clu a thing again. this is just a theory and possibility for what they might do, since the computer world is so big and might carry something like this.
Of course if this fact is true that means Clu could replace Kevin and take the company from Sam. With this he could create his dream of a perfect system in our world.