Disclaimer: Tron belongs to Disney.
Gone. It's all gone.
Clu has seized power, taking with his perfect will never go through the streets of Tron city, planning new structures while perfecting present ones. He won't get to write more programs to live in this place. What would the point be? Clu and his guards have derezzed all his supporters, will derezz any more he makes.
Tron is gone, he who fights for users, lost in a computer scream while he was hiding, to much of a coward to face his own creation. Lost trying to buy him time, get him to portal. In vain.
The portal has closed, and with it his son, his Sam is out of his reach. He will never see him grow up, will never play with him again, won't get to teach him programing. He will never see his son become a man.
He has the ISO girl, sure, a pale reflection of his flesh and blood. Someone to take care of, something to protect, the last of his hope.
What else is left for him? Loneliness, emptiness, madness. So he will teach the girl, and meditate, and try not to lose his mind to time.
A/N: one thing that struck me when watching Tron: Legacy, after squeeing over the pretty actors and the shiny world of the grid like a proper fangirl, was the contrast between the 80's Flynn, all genius with no respect for personal space and kind of a big kid, and the zen version, dim and quietly sorrowful. He was stuck in place for 20 years, no telling how long it was for him with the time difference between the grid and the outside. How does a man stay sane in these conditions?