- Learning the story of what happened between the first movie and the game by use of the Story Breadcrumbs and the spin-off comic. Flynn comes back from the digital world, begins to act erratically, appears to go insane, then ups and vanishes several years later (yes, this came out well before TRON: Legacy). No, he doesn't even leave so much as a pager behind in this timeline. Instead of being Put on a Bus to Washington DC, Lora Baines-Bradley is killed in a lab accident, and it drives a massive wedge between Jet and Alan. The best the grieving Alan is able to manage is to put what's left of her into an AI. Encom is in dire trouble, enough so that a shady-fly-by-night like F-Con can swoop in and take control, and while Alan is still considered to be an old mascot and something of a joke, he's been exiled to a lab in the basement instead of a token position in the boardroom, pretty much alone and friendless. No matter what timeline, the man does not catch a break.
- The Tower Guardian I-No choosing to stay behind on the dying, archaic mainframe rather than take his chances with modern computing, despite Jet's offer to try and save him.
I-No: I can't stranger. There's no place in the future for an old Program like me. I'd be swallowed up and de-rezzed before I could spit out my first routine.
- The flashback to Jet's arrest. You can tell that Alan loves Jet very much, but has a horrible time trying to express it. Jet, for his part, acts a bit like a Spoiled Brat. You can see a number reasons for why he's acting out, though. Alan's idea of love is to try and plan out Jet's future, to the point of being controlling. Jet doesn't want to be controlled, but is still willing to go through hell to try and save his dad. Worse is that the loss of Lora is the Elephant in the Room that both of them are hurting over and they can't even share their grief without it turning into an argument. It's clear they love each other, but they just don't understand each other.
- The Did Not Get the Girl farewell before Jet had to go back to the portal to the analog world and Mercury has to stay in the digital one. After all they'd been through together; the Game Grid, the Prisoner Bin, losing her at the reformat, finding her restored from backup with amnesia. The original Mercury (version 2.8.1) is brought back by Alan, but after they're reunited after their final battle with the DataWraiths...
Mercury: You're leaving, aren't you? This is no place for a User. We're too crude and rudimentary.Mercury: Promise you'll search for me.Jet: Of course.Mercury: (reluctant) I guess this is...End of line.
- Ma3a appearing to Jet during his final trip back to the Real World, fully aware as Lora, calling him "Jet" and not "Alan 2", and bidding him a motherly farewell.
- The opening scene of the comics. After seeing cyberspace, coming home, and realizing what being a User means, Jet didn't handle it well. Where his Honorary Uncle in the TRON: Legacy timeline set up a magnificent system and embraced the idea (well, until it blew up in his face., Jet went to Heroic B.S.O.D. and is shown as hunkering down in the shuttered arcade, afraid to even touch a computer. His speech to the psychiatrist even seems like a dark inversion of Flynn's speech at the opening of Legacy.
"It's an entire universe in there, one we created, but it's beyond us now. Really. It's outgrown us. You know, every time you shut off your computer...do you know what you're doing? Have you ever reformatted a hard drive...destroyed an entire universe? It's too much. It's too much power. I never wanted this. I never wanted the responsibility. I just wanted to make games."