Now, Koz has said that at least in his headspace, TRON 2.0 is resigned to the world of non-canon. E.G., alternate universe with no connection to Legacy. This includes "Ghost in the Machine", which was pretty darn cool, in my opinon.
Personally, I think everything can all fit together fine, with minor tweaks and connecting dialouge. And I shall explain it all, with dates.
1982: TRON happens. Alan and Lora get married, Jethro Bradley is born, and Kevin Flynn rockets up to be the president of ENCOM.
1983-1989: TRON: Betrayal. During this time period, Flynn gets married, Sam is born, and Kevin starts to develop the Tron System. Also, the events of TRON: Evolution Battle Grids happens, in which the player character, (which is actually Jalen from TRON: Evolution) becomes the first ISO champion of the Grid.
ENCOM is still experimenting with digitization, but since the MCP was destroyed, they lost correction algorithms that made sure things digitized properly. Since Kevin was in the MCP beam as it exploded, these algorithms were placed in his DNA, in his
code. Thus, things work fine whenever he tries to digitize, or when he's in the system, thus why his Disk was the master key in Legacy. However, in the 80s, it's all but impossible to extract anything meaningful from DNA. So ENCOM had to recreate it from scratch. During this time, Lora gets a job offer from Washington, which she takes (TRON: Betrayal). However, she was essential to the project, so she continues to work on it via correspondence.
Flynn retires from ENCOM to spend more time with Sam and work on the System, and ENCOM for a time goes to the control of Walter Gibbs Jr., the largest shareholder at the time. Alan didn't step in until later. 1989, TRON: Evolution, Flynn disappears into the Grid. Jalen was converted into a virus, that was eventually defeated by Anon.
1989-2003: First, 1991, Flynn is assumed dead, and ENCOM stops searching for him (TRON: The Next Day news clippings). During this time between then and 2003, Alan and Lora continued to work on the correction algorithms long-distance, resulting in Ma1a. However, it was imperfect, so Lora came back from Washington to work on it in person. In a digitization accident, she is fragmentally digitized into the system. Fragments of her data are used in Ma2a and Ma3a, Alan's way of trying to keep her alive. The correction algorithms were perfected in Ma3a.
During this time, Edward Dillinger Sr. made an attack on the ENCOM systems. Tron (a copy that Flynn left on the system) and a Light Cycle bot named Mercury repulsed this attack, and Dillinger realized he needed to attack ENCOM a different way. (TRON 2.0 Killer App (GBA))
Sometime after this, technology moved on, and the TRON program on the ENCOM systems was retired and put into storage.
Now, without Flynn's visionary leadership, ENCOM begins to flounder. Gibbs Jr. just didn't have the passion that his father did, leaving the company open to corporate takeover by F-CON, a front organization for Dillinger Systems (TRON: The Next Day, watch the news clippings for reference to them. Wanted to fit that in).
During this time, the events of TRON: Uprising are taking place on the Grid. Tron escapes CLU, and begins to train Beck. The revolution culminates in Tron's loss to CLU as Rinzler, fragmenting the rebellion, hence Bartik's desire to have Zeus unite the factions.
2003: TRON 2.0 happens. Jet Bradley and Alan digitize into the system, and uncover F-CON's real reason for buying ENCOM, and defeat them from the inside.
2003-2010: F-CON, under various legal and financial woes from their failed plot, falls. Dillinger Systems behind it? No one knows. No one even knew that they were involved. The stock goes back on the market, and using funds that Kevin left behind, Alan buys them in Sam's name. Sam probably began acting out about this time, making his at least yearly prank on the company.
Now, Jet and Alan have seen the system from the inside. They realize, that there may be a way to compile a program complex enough to realize (the opposite of digitize) into a human being. Programs that they previously tried to realize didn't work out well, in one way or another, due to their simplicity. So when reinstalling the system after F-CON, they come across a backup of Jet, which they compile into three packets, causing the events of TRON: 2.0: Ghost in the Machine.
At the end of it, Jet.exe (The backup Jet that they found) decides to remain in the system, but the concept was proven. They had successfully compiled a program complex enough to realize into a human. Using what they learned from Jet.exe, they were able to save Lora and realize her, bringing her "back to life", essentially. I'm sure the paperwork to figure that out was horrendous.
The Flynn Lives movement is picking up steam, giving us the ARG, with all it's real world events, including the press conference where Lora shows up, culmunating in the page that Alan gets.
2010: TRON: Legacy. Alan, recieving the page from the disconnected line at the arcade, and knowing what he knew from 2.0, he begins to put the pieces together, but he figured that Sam should be the one to investigate. Thus, Sam investigates the arcade, and Legacy.
2010-????: TR3N? TR4N? What does the future hold? I dunno, but I'll update this if we get a new installment!
Feel free to pick at it, give me discrepancies, etc. I welcome criticism.