The elf forest is cursed to repel humans and dragons: you were going to have to find a way to temporarily transform yourselves to get in. Had you gone, you would have found the Guildmeister made a deal with the elf king, corrupting him with a compelling orb and turning many elves into forest giants.
If you bothered to stick around and see out the revolution you had been fomenting, Jack and all the halflings would have joined in exchange for being granted all the land north of the lake as a halfling homeland and being named Count. Various barons would have sided with either the Duke or whichever Baron ends up leading the revolution. You would probably eventually find out that one of the barons was the Guildmeister's nephew.
Destroying the compelling orbs would require a flail imbued with the essence of the one incorruptible alchemist: Valian's real father. Whether he would live through the quest or not depended on you.
The secret weakness of the regenerating serum is poison damage.
Beneath the duchy you would find the ruins of a vibrant Celtic kingdom. They constructed a great artifact that would let them easily resurrect themselves from death: only old age could subdue them. The civilization fell when this artifact was corrupted by a green dragon, who transformed it into a soul-capturing device, and subsequently the souls of the entire civilization are now housed within the artifact. In reaction to this the elven curse was laid upon their own lands to the north.
The dragon spent a few centuries attuning himself to the artifact and unlocking greater powers within it, eventually gaining some near-divine abilities (such as granting spells to clerics) and so became The Deathbreather. He also learned how to make compelling orbs, which in addition to their other abilities also tag the souls of those affected so that they end up in his artifact and not the afterlife.
He is also able to observe surroundings through the orb, which means he witnessed the transformation of Sixteen into Baddhra and Tuvar. He also heard Mezentius' latest declaration of his true origins. Thus his master plan was set into motion: kill Mezentius and steal his soul. After, he'd use another liquid philsopher's stone to merge himself with the artifact and ascend to godhood.
The real Chancellor Amon is dead: the impostor is a green dragon who is one of the Deathbreather's children. Dying to him or any of the other green dragons you may encounter would result in your soul being imprisoned in the artifact.
Lysander's mysterious patron is Ligier, the Green Sun, who was born from the cut-out heart of the titan Helios during the great war in which Zeus overthrew his father. He would aid you in subtle ways which, unbeknownst to you, would help in his larger plot to swap places with Apollo so that Ligier shines in the sky and Apollo is imprisoned in Acheron.
The final battle would be against the Deathbreather who is a slightly more powerful ancient green dragon, with regeneration and a breath weapon that also deals necrotic damage.
If Mezentius died and his soul was captured, the Deathbreather would ascend into godhood, with the domains Death and Trickery. If his soul slipped away, The Deathbreather would have instead turned his efforts towards finding another demigod and simply capturing as many mortal souls as possible. If all the PCs died in one go, the world would continue and you would instead play as PCs from some other part of it who happen upon another branch of the wider plot.
Thank you everyone but Tip for playing. The game is over.