So I tried to kill the first opposing sovereign I met. I declared war and nuked him in the tactical battle. He wouldn't go lower than 1 HP no matter how many times I hit him, then he ran away from the tactical battlefield, teleporting back to his only city.

I then attacked that city, killing the defending hero. Strangely, although the enemy sovereign was in the city, he didn't participate in the battle.

Now the city is mine, but he's still sitting in it. I can't attack him, he won't die and he won't leave.

Savegame file can be found in Dropbox.