some shit

Most of humanity dies to a virus called Radical 6, with only like a 7th or 8th of humanity surviving. Sigma and Phi have the ability to swap consciousnesses with their own selves in different timelines, where they "jump" and replace the consciousness of the Sigma/Phi they're jumping into respectively, while the one that was in that body is sent to the body the jumping one jumped from. They need to have this power trained by basically being in near-death situations or choices.
Sigma and Phi are forced through a "game" that puts them in these situations constantly, and the only way for a true good ending where everyone lives is for them to manage to use this power. It works and Sigma finds out that his own consciousness is meant to jump back in time, create the game, and then swap back so the younger self does the game, learns he makes it, then makes it, etc. It's a self-sustaining paradox. (It's confusing and I'm simplifying the whole loop, but that's the important stuff for the game)
After said consciousness goes through building the game for himself, the jump that puts the younger version of himself into his body at the start of the game also puts the older version at a time a few days before the virus outbreak, at the location of the outbreak which is when/where ZTD takes place. (This is why the "Chronological" timeline isn't that important in terms of viewing, it's focused on the timeline of Sigma.) In this facility (Don't worry, I'm not spoiling anything that isn't in VLR) there are two important timelines. One is the timeline where he succeeds in stopping the virus, which is basically his goal, and the other is the timeline where he fails leading down to the VLR timeline. He knows at the start of ZTD that the timeline where he fails leads to him losing his arms and eye (which are later replaced with mechanical parts) but doesn't have any memory of how for some reason so he can't do anything to prevent it.
So for a recap in the order of how Sigma's consciousness went through it all: He played a game and learned how to swap himself across time/timelines, went back in time a little to succeed in the game, went back in time to build the game, and went back in time one final time to a few days before the virus escaped in order to stop it. There's probably some important shit I missed but I've already written enough for something that might not even be read.