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I now have the same problem.
I provided excellent troops for both Isabelle and the Necromancer (I don't remember his name). Isabelle is in the first Necropolis castle, "Mythograd."
She's just sitting there, guarding it. You never know what might happen =)
I killed the elves with the Necromancer. It just happened that way.)
So, I captured two NECESSARY castles, the ones with the staff and the cloak.
But where is the third one???? I can't find it. I've searched all the portals, even the one-way ones. Nothing...
And another question: do the thousand skeletons have to be warriors, or can they be archers?
You can see 3 magic castles from the mage's hut near Mythograd. The fourth one is in the northeast corner of the map.
The 1000 skeletons can be either simple skeletons or archers.