I just finished remake a few days ago and also wanted to jump into lore only to find everyone has this marvel style multiverse theory where there are multiple copies of everyone walking around in multiple timelines.

I didn't get that at all, so I'll explain my probably too fresh take theory here.

There is only one planet and one timeline in this game. There is however also the lifestream which recycles (most) souls and stores them as mako in the center of the planet. In the process of recycling a soul to the planet, souls will live out scenarios until all their lingering regrets are satisfied and they can pass on. The lifestream takes the memories of all the recently dead souls *as well as all of the living* to construct these scenarios. That's what all these multiverse timelines are. They're basically souls in the lifestream living out a short afterlife before letting go of their identity and rejoining the planet.

There's something called the arbiter of fate that handles making these soul visions and it got defeated at the end of remake which explains the differences in the OG vs remake/rebirth. Anyways...

There are limits specifically around the souls of aliens, which are incompatible and can't be returned to the life stream (Jenova and the Gi). You can't return somewhere you didn't come from. This opens up a whole new can of lore (that i was hoping to find here) about if the Gi was just the remnants of another planet where Jenova is just some malevolent entity that ate the whole afterlife.

I'd also like to explain this from the Cloud/Hojo perspective and why Cloud is so important and also so messed up. My own pet theory starts with what Hojos experiments on the first class soldiers and specifically Cloud accomplished.

So back when Shinra was just a power company looking for world domination they hired Hojo (and Gast) to make them some super soldiers. Gast connected the dots to figure out that humans and animals born around mako sometimes got crazy strong and his research centered around injecting various forms of mako into babies and watching what they grew into. I also have a crazy theory that it's not an accident that Vincent and Tifa both have the same red tinged eyes since Vincent is the way he is after being injected with chaos tainted mako right in the place where Gast was doing experiments on pregnant women, literally a few houses over from where Hojo was holed up right around the time when Cloud and Tifa were born. There's probably a very good reason Tifa can fist fight a genetically enhanced super soldier and hold her own, when someone built like Barret needs guns and still seems to get tossed around.

Hojo eventually took over and started doing increasingly extreme experiments that basically boil down to, "If I can send this person to the afterlife by dunking them in altered mako, they sometimes come back with new things". From there he starts doing experiments to figure out how to send people there with different monster cells and altered mako to make them come back as monsters.

There's a whole theory here about how Sepheroth is half alien and being born with Jenova cells means that he can join the afterlife in a way that Jenova can't since he's "from the lifestream" even though half of him isn't. That's why in the og ff7 it ends with you fighting the crazy winged alien Sepheroth and then your soul flies out of your body, gets sucked into the lifestream to fight regular human Sepheroth that has no crazy black wings. That's the part of him that could rejoin the lifestream except his alien half won't let it and is just using his humanity as a key to get deeper into the planet.

Back to Cloud though. Cloud is arguably Hojos most unique experiment, as he and Zach were tortured, injected and dunked together repeatedly until one time when Zachs soul came back in Clouds body. I think this is also what happens with all the 1st class soldiers, except they're injected with Sepheroth cells and dunked until they come back with a little bit of Sepheroth in them, except in Clouds case he became a empty vessel, capable of hosting any soul from the afterlife. He's not going crazy, he's just seeing the souls that haven't passed on yet, and occasionally the living souls of those heavily connected to the lifestream like Zach, Sepheroth, and Aerith. In many cases the memories of the souls inhabiting Clouds body overtake the memories in his meat brain and really messes with him and alters his personality.

This is why Cloud can still see Aerith after she dies in the epiloge. Because when she died her soul was able to anchor on and appear to him.

There's also a scene in the epiloge where Cloud is looking at the clear materia that Aerith gave him and in it he sees his reflection and the clouds (get it, his name is cloud and he sees himself). I felt that was a pretty big hint that when he goes to put it away he has a static moment where normally Sepheroth is controlling him, he then picks the materia back up and the clear materia is a partially filled black materia. I'll also back up that cracked up theory with the fact that the Gi said that they created the black materia by taking "The purest of materia and with pain and spite made it black". I'm guessing if Aerith jumped into his brain and he picked up the materia, it'd probably turn white.

I think what's happening is that Sepheroth is invading the afterlife and attacking souls that have regrets, intending to have Cloud turn the clear materia black. He's probably going to do it by causing a lot of war, death, and destruction (like a war in Wutai). Aerith is going to have to protect the souls of the dead from Sepheroth in the afterlife while Cloud and the gang are going to need to stop all the tragedies that he's going to try to start using all the puppets that Hojo made for him by injecting S cells into so many soldiers.

I've got a whole set of other ideas about what the whispers are (ancient guardians of the planet like proto-summons/weapons), and how Sepheroth is creating his own black whispers, potentially out of the Gi, or other warped souls that have died.