What if there was a twist to this story? Both of you being Dragonborn, maybe during your battle with him as you issue the "final blow", he issues his own special shout that allows his knowledge and soul to switch places with the target. Next thing you know, you get blacked out and wake up very injured, almost dead. You now have to set on a quest for this shout he had created, learn it, and quickly switch bodies again and finish him off.

Now, this would be quite a twist. But what would be a very funny but frustrating troll is if this same thing happened, but Beth found away for it to kill your body instead of his and you're stuck in his body.

Lol sounds like trying to pull a move from Dishonored.

It'd be interesting but since the game doesn't really have much in the way of restraints for missions I don't think Beth would let you run around as Miraak and he you.

s

"Why the hell were you at that tavern wench's place all night???"
"Baby, I swear to The Eight I don't know! Great-great grandpa was in my body! No, really! I swear! Wait, please, you can't shoot me, you don't even know how to work a crossbo-*twang*"

I've only watched 2 missions of Dishonored so this all came from my head. As far as that, maybe all this would be confined in the new island, you couldn't leave to skyrim until you got your body back.

Restraints on not being able to leave isn't Skyrim's style. A times the game is TOO free.
But unless you have to chase him down in Mora's Library then it could work.

Or... what if he devours your soul, and you have to fight your way out of his soul-intestines and against the souls of devoured dragons in his soul-grinding bowels?
(This isn't a serious idea)