So first, to reiterate for a lot of people that seem to have forgotten, the "Sephiroth" we are seeing in Remake and Rebirth is Jenova. Sephiroth himself is still trapped in ice in the Northern Crater and will stay there until Cloud shows gives him the Black Materia in part 3. You might see me say Sephiroth and Jenova here interchangeably, but the villian we are dealing with in these thus far is 100% Jenova. It looks like there are multiple "versions" of Whispers now. The grey ones, "Arbiters of Fate" that we destroyed at the end of Remake seem to be the kind that are preserving things as they should have canonically happened in OG FF7. The white versions seem to be servants of the Planet and do whatever is necessary to protect it. The black versions seem to be pawns of Jenova to do her bidding. At some point (possibly the ending of Advent Children), Aerith and Sephiroth/Jenova became aware of the existence of multiple parallel worlds and Jenova is trying to undo her destruction and merge ALL the worlds. (Gilgamesh, known for being a realm traveler having such a big role in Rebirth is no coincidence, imo). Aerith in Remake seems to have complete knowledge of what is going to happen up until the end when the grey whispers are defeated, at this point she loses that knowledge. At some point she seems to have shared this power with Marlene who also seems to know certain things that "should" happen. Rebirth follows the plot of OG FF7 relatively faithful up until near the end where Aerith and Cloud seem to plunge into the void. They then wake up in their bodies in the alternate Zack world, as evidenced by the same Stamp appearing here as Zack's previous scenes. Meanwhile Zack is stuck debating whether to save Biggs, confront Hojo, or stay with Aerith. We get glimpses showing the outcomes in each scenario being a different world, evidenced by the Stamp in the Biggs' scenario being a THIRD variant. In the Forgotten City, Jenova uses the fake black materia to open the gates and worlds begin to merge, so Aerith is killed but she is also saved, and Cloud flashes between them multiple times. However in the world of Rebirth, she is definitely killed. Her white materia drops into the water just as it did in OG FF7. But Cloud, whether he realizes it or not, is now in possession of the white materia from the Aerith of Zack's world. Zack is able to hop between worlds momentarily to help Cloud fight Jenova. Aerith from the Zack world helps Cloud fight "Sephiroth" in the final battle, as he departs the worlds begin to separate once again and Zack is returned to his world, while Zack's Aerith vanishes and Cloud is returned to the Rebirth world. Cloud continues to phase between his world and the alternate world, evidenced by him seeing Aerith and the rifts in the sky while no one else does. Meanwhile Cloud is now in possession of the *real* black materia, and Jenova is still manipulating him into delivering to Sephiroth in the Northern Continent.
Rufus is aware, at least by the end, that Lodbrok is Jenova/Sephiroth and Shinra has been manipulated into war with Wutai yet again. Not much idea on Viceroy Sarouf, but if he was indeed an ex-SOLDIER as Yuffie said he has been injected with Jenova cells and can assumed to also be a Jenova puppet. Hojo seems to just want to turn everyone into a Jenova puppet to see if his mad theories come true, and by the final game he'll probably inject himself with Jenova cells to become a puppet himself. I'm expecting a Shinra/Wutai war to be a big part of part 3.
I get why some people might be apprehensive about the whispers taking a large role here as more Nomura nonsense but it didn't bother me here. As apposed to the ending of Remake, where my mind was full of fuck because of all the new possibilities being introduced here, I was able to follow the ending of Rebirth a lot easier with the added context.