The upcoming sequel will continue the story of Flynn the younger.
Disney and Garrett Hedlund confirmed that the star of TRON: Legacy will be playing the part of Sam Flynn once again in the new film. No word if Sam will once again be the protagonist.
It was originally announced that Eddy Kitsis and Adam Horowitz, who co-wrote the first film would be penning the new sequel, but those duties were taken over by David DiGillio, who finished the first draft. Now the script is in the hands of Eragon writer Jesse Wigutow. Jopseph Kosinski has already been signed on to return as the director.
All we know about the plot so far is that it is intended to tie the franchise up into a trilogy, so we should expect a certain level of dénouement. It will be interesting to see if the studio picks up from where it left off in Legacy or if another huge jump in time is made, perhaps even skipping down to the next generation of Flynns; the children of Sam and Quorra, if that's even possible.
What would the children of that strange union be like? Half human, half software-made-flesh; what kind of social issues would they face? Where would they feel at home? I think this would be a particularly compelling part of the canon to explore.
No word on any of the other actors from the previous films, but it's hard to imagine that they could do it without Jeff Bridges or Bruce Boxlightner. Olivia Wilde would not be a necessity to a new plot, but I don't think anyone would mind her return either. The character she played was one of the most interesting, if implausible addition to the canon that was made by the second film.
No production or release dates have yet been announced for the as-yet-untitled conclusion to the TRON trilogy.