Instead of fighting and killing him like you were meant to, you decided to do what you’re best at. Saving.

You fought Herma-mora, defeating him, thus releasing Miraak and yourself from his grasp. You put a stop to Miraak’s plans, and removed his control over everyone on Solstheim.

He despised you, of course, you ruined his plans.. and yet, he finds himself thinking about you. It’s unfortunate how the heart works sometimes.

He appeared before you again, watching you silently as he did sometimes. His body wasn’t exactly all there, as he no longer did have a physical form.. but nonetheless, he watched over you. It could’ve been because you saved him, or because you were the last Dragonborn.. but it could also be because of his feelings for you.