Assume the international version never existed. That's the first step. :P
Given the nature of this thread, spoiler warning is obviously in effect, but the game's been out for over 15 years.
AC3 is a simulation. What we can confirm is the following:
- Simon Orestes Cohen was a real person in 2040.
- Yoko Martha Inoue was also a real person, and was killed. Simon had some kind of relationship with or feelings for her.
- Abyssal Dision was also a real person. I don't know how to discern the info on the Yoko and Dision articles between what was in the simulation and what was real, but Simon blames Dision for Yoko's death. Dision was dead by the time Nemo was created, but continuing to live on through the Electrosphere, and I believe Simon created Nemo to kill Dision's Electrosphere copy and make sure that he was erased from the world.
Otherwise, everything else featured in the simulation is up for grabs on whether or not it was real. Simon's words, "time to release you into the real world", I have no idea what he means by that. The simulation resided in the Electrosphere, and the ending digital screen says that everything was purged, so it's likely that "releasing into the real world" meant "deleting your very existence for good". Simon was clearly crazy so I don't know. :P
No information is available concerning what actually happens between 2020 and 2040, or during or after 2040.
According to the United Galaxy Space Force retcon and the United Galaxy Space Force article on the Galaxian wikia, by the year 2090, all of Strangereal's governments banded together to create the United Galaxy Space Force, an overwatching government for all of Earth due to the planet reaching its population saturation limit. They became a militaristic force (think of the United Nations Forces) when they realized their starships were being attacked. Cue the Galaxian games and all subsequent games in the UGSF series.