Flynn is creator of the grid and is also the spiritual hero/christ figure. He is creator, yet sacrifices himself to save both the real world and his creation.
The creation of the grid was done by a three people, Flynn, Clue and Tron - a trinity.
Clue was created in Flynn's own image, but fell into corruption.
Clue picked up an apple in Flynn's headquarter's. The apple reminded him of his fall.
The apple also represents knowledge of good and evil - the ability to make correct and just judgments. Flynn, after all this time, now realizes that he did not aspire true perfection. He realizes now that true perfection would have been to sacrifice his own interests for his loved ones - namely his son.
Flynn sacrificed himself to preserve a new and improved humanity - he ensured the last remaining ISO, Quorra, would live.
Finally, Sam, the action hero, was a true super user (I'm sure this Linux joke has already been made).
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