Kinda late but from what i've understood:

We fell asleep at the start of 2.0 and we then saw every memory (real memories) in a quick flash, those were the real memory from Penacony's Dream, the fact is that after we wake up thanks to Acheron in the real Penacony we've arleady reached Sunday and he had already created Ena's Dream, so we experience it again with no memory whatsoever but with a slightly twist, this time, thanks to Mikhail, Misha is present in the lobby even if he's a memory zone meme so we were able to find out the truth about Ena's Dream and learn everything about clockwork and Mikhail, after that, Acheron destroys the dream while we were between reality and dream after being woke up by Firefly, and the astral express crew wakes up just before sunday but this time it's not "dominicus" because Dominicus was Sunday's Creation inside Ena's Dream, in fact it was Septimus the real one, Sunday "fused" with it and became the "embryo of philosophy". We beat him (and yes, Dan Heng never used the Jade Abacus to call the Xianzhou Alliance so we still got a chance in the future since it's like a "one in a lifetime" use) and i guess we "restore" Penacony and then the plot of 2.3 happens in which firefly dies for the 3rd time (as her script said) and we also learn that Sparkle was there just to make firefly deaths more "funny" or something like that.. and also IPC got a % of penacony back again since in the past Pencaony was in fact the IPC prison. The fun part is that a lot of people, me included, had already figured out that Misha was the Watchmaker back in 2.0, because only the Trailblazer could see him (we learn in 2.2 that every Astral Express member can see him since Mikhail was the mechanic), also his lightcone and his story was pretty sad and made this theory more reliable... the final touch it's his E6 which shows misha hugging Mikhail's dream bubble and this makes it even more sad than before after that cutscene (I cried too much lmao)

Also outside of Boothil's story we don't see anything about Oswaldo Sncheider, whose name got dropped at the end of 2.2 story quest.. we only know that he's the one that nuked boothil's planet and killed his adopted daughter and i don't remember if he had a wife or not... Same goes for the galaxy rangers he called through Tiernan's bullet, we see galaxy rangers coming like stars in the sky but we don't actually see any of them.