The new Super Lightcycle seen for the first time in this game was designed by Syd Mead, the man who designed the original lightcycle twenty years previously.
The game ties up a lot of loose ends about what happened in the 20 years since the events of Tron (1982) took place. Flynn did tell Alan what had happened to him in the hours he spent in the computer, and it was likely that Alan believed him. Alan apparently married Lora not too long after the movie took place (never going back to Flynn) and they wasted no time having a son, Jet. A few years later, Lora died in a digitizing accident.
Disney had been planning to do a Tron game for many years, sometimes even going as far as creating technical lightcycle demos, but nothing usually ever came of it. It was a chance meeting with a Monolith employee and Disney Interactive (later creating Buena Vista Games) that set the stage. Everyone at Disney was impressed with Monolith's game "No One Lives Forever" and they were willing to let Monolith take the Tron license for a spin.
Through in-game emails, it is implied that the 'Ma3a' AI is at least partially Jet's mother, Lora. She was experimenting with the digitizing laser (following the events of Tron (1982)) when she was partially digitized into the computer world. Ma3a, interestingly, is integral to the rediscovery of the "correction algorithms" that Lora was attempting to rediscover at the time of her accident. Cindy Morgan is the voice of Ma3a, who also played Lora in the original movie.
Steven Lisberger served as the game's consultant. He personally verified the opening digitization sequence as canon to the TRON universe.