The good guys go around the four towers in Chapter 7 as you know, battle the Ouroboros enforcers on top of each towers, of course with the enforcers revealing a bit more of themselves in the meantime. Most important story being that Renne is that way because she was abandoned by her parents to some very bad people who abused her, until Ouroboros wanted the resources of that particular criminal organization and destroyed the organization & saved Renne at the same time, which made her think that Ouroboros is her "real" family and that she owes them for getting her out of that hellhole, so she does whatever is asked of her. The rest of the enforcers' stories were kinda meh in comparison.
Anyway, the enforcers were basically deactivating the towers which were the final "locks" for the Aureole. After going through all the towers, a huge floating city appears in the sky, Aureole. It causes a supermassive orbal shutdown phenomena that expands past Liberl's borders. Liberl is in chaos. Chapter 8 is mostly about dealing with that shit, going through all of Liberl. It befalls the bracers to go around taking these devices to every city that negate the orbal shutdown phenomena (in a very small scale) and at least allows the bracer guilds to communicate with each other (the army uses the same things too).
After you've done that, you're asked to go to the capital. Before getting there, the enforcers start a full-blown attack against Grancel in an attempt to take the queen & princess hostage. With some help from surprising & not-so-surprising people, you spoil those attempts, at least. But before they can celebrate that for too long, it comes to their attention that Erebonia (the country who tried to invade Liberl before) is amassing non-orbal tanks on Liberl's border. The bracers are sent there to act as a kind of neutral party in whatever happens there. At first, the Erebonians believe the orbal shutdown phenomena & Aureole are some new weapon Liberl is attempting to use against them, but with the help of Prince Olivier (yes, he's revealed to be one of the princes of Erebonia) and Estelle's father coming to the scene with that state-of-the-art airship (don't remember the name atm), which that genius professor has gotten to work despite the OSP, they manage to buy some time before Erebonia starts their "we are just making sure you aren't up to any funny business" invasion of Liberl.
Chapter 9 (final) is then about the crew of bracers & some other people flying up to the Aureole and spoiling whatever plans Weissman has there. Prior to getting to Weissman, you fight the enforcers again. Schera's old friend dies, Beublanc runs away, as does Zeke's friend, Renne fly's away on her mech after another talk with Estelle but it's implied she doesn't return to Ouroboros but goes somewhere where she can think for a while. Loewe & Joshua make up on top of the central tower, but Loewe sacrifices himself near the end in an attempt to create an opening for the good gang to beat Weissman.
During Chapter 9, it turns out Aureole was this kind of "paradise on Earth" type of deals where a kind of super-advanced AI took care of every person's needs & basically controlled everyone's lives. Except that kind of made people worse since they could indulge in all kind of corruptive-in-the-long-run behaviour (IIRC people became addicted to stuff etc.). In time, some people (including the ancestor of the current royal line) came to the conclusion that the Aureole wasn't a good thing, so they came up with a plan to get rid of the Aureole by shifting it into another dimension (since going head-on with it would be suicide due to the resources it controlled). They descended from the Aureole on to the surface of the planet and worked in secret. Even though the Aureole fought back after it figured out what those people were doing, they managed to succeed in their plan and suspended it in another dimension (the thing that happened in the end of the first FC was the first "lock" keeping Aureole trapped in that other dimension, the tetracyclic towers were the second line of defense against bringing it back). But yeah, now Ouroboros/Weissman brought it back. Weissman thought that the kind of ultimate rule that Aureole had would be swell, Estelle & co didn't. Final battle ensues. Weissman merges with the Aureole -> you still beat him. The flying city starts to fall apart and in the confusion Weissman still escapes. He doesn't get far before Kevin stops him & kills him, revealing in the meanwhile that he's a part of this kind of "black ops" unit of the Church who basically do the dirty work of the Church, like getting rid of horrible human beings like Weissman, if need be.
Back to Estelle & Co. While they are escaping, they get separated from the rest. They try to find another way to the airship but before that all their ways forward are destroyed. They think they will die, have a sweet moment with each other. The structure beneath them collapses, they start falling from the sky, only to be caught by Cassius who is riding the dragon we saw earlier in the game. The end.
That's about the gist of the larger storyline from chapter 7 forward. Writing about smaller details would make it way too long.
