One idea I had was to supplement the few known agents (who could all be dead by the end of the MQ) with returned Ascended Immortals that were in Paradise before you killed Mankar Camoran - specifically the ones running the torture cages, rather than their victims. Eldamil would become the head of the Inquisition - Nirn's Torquemada - trying to redeem himself but overdoing it a bit, due to his judgement being no better than when he joined the Mythic Dawn in the first place. There's also opportunity for false accusations, planted evidence, etc. to make a good story of it all. The quest sequence is likely to end with your having to kill Eldamil to stop his excesses.
Since closing an Oblivion gate spits out the hero and any followers, it seems reasonable that the various portals to Paradise might regurgitate those who entered them when Paradise is destroyed. So a number would re-appear in the Lake Arrius Caverns, and other places around Cyrodiil, at the time you killed Mankar. By the time the Main Quest ends, they'd have scattered back into communities all over the place. Although they enjoyed(?) immortality in Paradise, that would no longer be the case once they returned.
Any lore problems that anyone can see with this scenario?