Ok, apologies if there are any inconsistencies or incompleteness in this, it has been a while since I played and the plot was super complicated.
As you saw from the twist, the events of the past and the events of the present are being played out simultaneously, with Akane in the first Nonary game observing Junpei in the second Nonary game, 9 years later. This happened due to what the game calls a 'morphogenetic field'.
This morphogenetic field was created while Akane in the past was in the incinerator. She suddenly made that link with the future, projecting herself 9 years ahead, able to observe Junpei in a similar Nonary game situation. She was able to observe Junpei follow several paths - on some of these, Junpei failed, meaning Akane in the past would have died. However these are just possible futures - when the current path failed, Akane in the past started again, watching Junpei take a new path, guided by the clues she had learned from the other paths. Eventually Junpei took the path that gave past Akane the solution to the incinerator puzzle, allowing her to escape. So she never died in the first place, these were just possible outcomes that Akane observed, but did not really happen.
(Whenever you were on a path where June could not exist, due to Junpei getting into a situation where he could not save Akane in the past, June would suddenly develop fevers and headaches. You could say these moments were approaching a paradox, and that marked failure for that path. But no actual paradox happened, Akane from the past always survived, these were just possible things she observed)
Since Akane survived, she then set up the second Nonary game herself, as Zero, to ensure the future she saw comes true. The whole thing was to guide Junpei to that screen in the incinerator, to solve that puzzle for her younger self, to prevent a paradox. However older Akane also participated in it herself as June, as another function of the game was to get revenge on the perpetrators of the first game.
About Seven, I guess that was left open. My belief is that he and Santa/Aoi knew the truth all along, and that they were Akane's collaborators in setting up the second Nonary game.
I believe his amnesia was real (due to the soporil drug) but after recovering his memories, the bit about Akane was a necessary lie.
Virtue's Last Reward touches briefly on a few parts of 999's story and only adds a tiny bit to it, an epilogue to the true ending - *super spoiler* - an elderly Junpei participates in VLR's nonary game, and is reunited with Akane at the end.
Edit - Akane pretty much HAD to set the future game up in the same way as she saw in the past. She couldn't miss any detail, she had to make the future play out the same way. That includes killing certain people, and letting Ace get hold of a loaded gun.
It MIGHT have worked if they did it differently, like, only had one room, tried to get Aoi to do it, etc, but could she really afford to risk it?
Don't forget also the plan was to get revenge on the Cradle Pharmaceutical executives.