I think I'll try predicting the rest of this fic. I don't know how close I'll be to the actual plan, but I've reread this story so many times, and I have some experience writing myself so I just want to try.
So, the coming conflict with the S9 will probably be the beginning of the final conflict, I think. Or maybe second to final, depending on how you look at it. When that starts, everything will just keep piling up. Uber and March will use the opportunity to act, and probably make themselves and the Butcher and maybe a few other parahumans into something like Titans (not actually Titans, because Zion is still alive, but something similar), which they'll be able to do because March is bullshit and Joe is deliberately choosing not to know about Noelle, but, in the end, it won't actually matter all that much because Joe is far more bullshit. But in the act of stopping whatever happens he'll have revealed enough of himself people realize their Thinker predictions are wrong and the Simurgh will descends soon afterwards (with actual prep, and maybe help from the other Endbringers). Again, won't matter. Joe will just beat them all anyways (actually, I'm kind of rooting for Aisha being the one that actually offs the Simurgh - just shoot her with ten thousand Gant lasers Aisha, you know you want to!), but in doing so he'll have revealed enough about himself there's no longer any reason to hold himself back, so he'll deploy, across the whole planet, maybe even across multiple Earths, and start saving people, all the while getting Panacea, Flechette, and Taylor up to speed in case he needs them.
Zion will eventually notice, and decide to act. Like an Entity, this time, with actual motivation, instead of a suicidally depressed god. That means Joe, or rather the entire Forge, will have to fight almost the entire Shard network at once, all the while evacuating the planet and probably many parallel earths at the same time. This will be a battle. A battle to see how much damage the Entity will do and how many people will die before the Celestial Forge finally overpowers him. Maybe Taylor will help, maybe not, probably not the same way as she did in canon, but Joe could probably make an army for her to coordinate. I doubt Flechette and Panacea will be needed. Everything they can do the Celestial Forge can do. Taylor still has something to contribute though, but I think it depends more on convincing Queen Administrator to rebel than anything else. Ultimately, I don't really know how it will end, but given the bullshit that is the Celestial Forge I don't think losing is even on the table, no matter what happens. It's all about how many people can be saved, and Taylor can maybe be of help here.
Then, in the final chapters, we'll see some scenes of Fleet, Survey and the Matrix as they scour the rest of the local multiverse cluster for the other Entities. The nature of the Celestial Forge will probably be explored a bit more, we'll see the aftermath and what kind of world Joe wishes to create, explore some more characters and reactions and relationships, then... finished. I think.
That's my best guess at least.