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These are recommendations made by Tropers for Tron fanfics, all of which have to be signed to stay on the page. Feel free to add a fanfic of your own to the list, but remember to use the template found here.
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Synopsis: A continuation of Tron: Legacy, involving two hackers who break into Encom's systems one night to steal a file. They're looking for the "Tron" video game file, but end up with something called "Rinzler"...
Comments: A brilliantly written ongoing fic with an engaging and fascinating storyline. The O Cs in this story are genuinely likeable and feel like they belong in the Tron universe, and the ideas behind the story (and the way it plays out) are pure genius. It also explores programs' experiences with coming into the user world, including things like how they learn to eat, use their muscles, and deal with things like different sensations and not being connected to everything. In short, well worth a read.
Synopsis: Clu outsmarts Kevin Flynn and enters the real world, alone. Here, he sets up the invasion by masquerading as Kevin Flynn and arranging a setup that will lead the users themselves to invite programs to invade them. In short time, he reveals his real Magnificent Bastard persona and the fate of the world is sealed.
Comments: The darkest Tron fanfiction I've read, with an enthralling and disturbing take on Clu.
Synopsis: Eight years after he rectified the entire Earth, Clu sets up to rectify the entire universe. During his multibillion-year mission, he discovers and solves some fundamental mysteries, and uses them to his advantage.
Comments: Less dark, but more philosophical than its predecessor, with a few Mind Screws along the way.
Synopsis: Jet Bradley and Sam Flynn live in a world of computers, their entire life built around them, but the idea of electronic beings living within them was one they never comprehended, not even when they find themselves smack in the middle of it.
Synopsis: Tron deals with inevitable guilt with Sam.
Comments: I can't really summarize things all that well, but I'll say this: this story is one of the best continuations I have ever read. The writing is superb, and shirozora has an excellent grasp of each character involved, and the OC's are also fleshed out quite well. It's completed, and the author is currently working on a sequel.
Synopsis: While taking a coffee break at Encom, Sam remembers his father and how he aged in The Grid. Soon enough, Sam is faced with a dilemma about his future with Quorra... He chooses to stay with her, albeit aware that he will gradually age and die while she will remain her 20-something self.
Comments: Unlike many other Sam/Quorra shipping stories, this one not only portrays it in a mature, realistic matter, but also uses accurate portrayals of the characters. The fanfic also explores the ideas of aging and angst and how it will affect Sam's decision.
Synopsis: There is more than one way to break a man...even ones made of digital code.
Comments: I hesitate to put this under "shipping," aside from this containing some twisted elements of Foe Yay, but Users, it drips with the stuff. Clu is an inventive bastard. He'd know that he wouldn't be able to break Tron using pain, which means "pleasure" is much more efficient tool.
Synopsis: "I gave [Lora] up because there was someone else, here, that meant more to me than any user. I gave her up for Tron. Tron is why I've done what I've done, and am doing what I'm doing. He is why I'm sitting in the poorly lit bar, watching as people come and sit around me, their eyes and ears waiting to hear my story that I don't want to tell, but will tell all the same."
Comments: Yori's absence from TRON: Legacy has made greatFanfic Fuel. Ridyr's story takes the fuel and adds a lit match. It unravels events from the coup to the end of Legacy, casting her as a member of the Resistance, through capture, conscription, and the eventual freedom she and Tron win for themselves. And it handles "Rinzler" marvelously.