Kevin Flynn was a rising star at Encom, creating several video game programs on his own (Space Paranoids, Vice Squad, Matrix Blaster, etc) before the private memory cache he had set up to store these programs was coopted and by Edward Dillinger, Sr., which led to the latter's meteoric rise to Senior Vice President of Encom, and Flynn's eventual dismissal from the company. After leaving Encom, Flynn would eventually launch an arcade venture, but he would never really stop searching for the files that would prove that he was the creator of the video games that Dillinger claimed as his own, which would lead to the creation of the first Clu (Codified Likeness Utility) program.
Flynn's forays into hacking the Ecom mainframe would be detected by the Master Control Program, and the eventual deresolution of the first Clu. A blow to Flynn's plans, but that wouldnt at all dter him. It only brought him once more into contact with Lora Baines and Alan Bradley, and the three of them hatched a plot to sneak Flynn into Encom and hack the mainframe from the inside, leading to the MCP's sending Flynn down to the original Grid and his adventures with Tron, Ram and Yori, leading up to the destruction of the MCP, his return to the real world, and the evidence which would vindicate his claims., get himself reinstated at ENcom, and eventually become one of the company's largest (if not the largest) shareholders.
Kevin Flynn would also become a father, marrying and eventually having a son, Sam Flynn. Yet nevero ceasing for laying the groundwork for a 'digital frontier to reshape the human condition.' Flynn would become more absorbed in this task, creating the second version of the Clu program especially for the task of aiding to shape the Grid to perfection.
But after the death of Sam's mother, Flynn would become progressively detached from the real world, choosing to spend more and more time on the Grid, to a point which would almost border on the obsessive. This would lead to the discovery of the ISOs and his thought that he had made a breakthrough that would effectively change the entire world.
However, it would not be much longer before Kevin Flynn disappeared in 1989. Some thought possible foul play, some thought he'd simply just disappeared for reasons of his own... but the truth would come much later... much later being 2010, and the discovery by his son that Kevin Flynn had been trapped in the Grid he worked so hard to build up, trapped there by the program of his own creation, Clu.
It would appear as if Flynn sacrificed himself by reintrgrating Clu into himself to save both his son Sam, and Quorra, the last of the ISOs, allowing both to exit the Grid and return to the real world.