After a hiatus, I recently got back to playing Skyrim. While mulling over what Hermaeus Mora may have wanted from Miraak in the long term, something disturbing occured to me. What if Mora had intended to control the dragons of Nirn?
A brief summary of Miraak's life. Once a dragon priest, Miraak came onto one of the black books belonging to Mora. As we know, Daedric relics aren't found by mere coincidence, but none the less Miraak used the book to meet Mora. In return for Miraak's servitude, the Daedric prince taught the former priest the power of bending dragons to his will. Miraak rebelled, was defeated and Mora drew him into his realm, Apocrypha. There it can be safely assumed that Mora preserved Miraak until the time was right to unleash Miraak onto the world, which was during the time when the dragons returned to Nirn and the last Dragonborn would be born. This gave Mora enough time to further bend and mold Miraak into the tool he needs. The last dragonborn would have been a trivial matter to the prince, a mere child that knew nothing of his or her destiny, something easily disposed of.
Now what if Mora had intended for Miraak to not destroy, but instead conquer Alduin? Miraak may have said that he intended to destroy Alduin someday, but Mora may have easily steered him to do otherwise. If Miraak could have bent the will of Alduin, the 'head dragon', then Mora could have controlled Alduin through Miraak and through Alduin the other dragons. Miraak's arrogance would have left him to believe that he himself was the master of all dovah, while in fact it would be Mora who pulls all the strings from the shadows. Dragons are wise and ancient creatures, fitting well within Mora's sphere. And since neither the Aedra nor Daedra interfere directly, their minions would have had a very hard dealing with a bunch of dragons.
Since the (player) dragonborn did become powerful, Mora may have ditched the troublesome Miraak in favour of controlling the last dragonborn. If Alduin was not yet killed, Mora could have used the dragonborn to conquer Alduin instead. And if Alduin was defeated, the dragonborn was now recognized as the stronger dovah, who may yet dominate the dragons with Mora's guidance.
So what is Mora really up to? Does he want to corrupt and control the dragons? It would be terrifying to imagine what a dragon could do with some sunday-schooled teachings from the Prince of Knowledge. That old Hermaeus may have been up to a lot of trouble, and still may be up to a lot of trouble, if he gets his way.
Note: ignore the fact that Alduin cannot have his will bent in the game, these are likely gameplay mechanics alone to prevent quest-breaking; Alduin still is a dragon and a dovahkiin powerful enough to defeat him, might well bend his will also.