Shiv said:
The souls now are trapped within some horrible, nasty prison realm. A plane aligned with the necromancer. A demi-plane. Whatever you want. What form they take there, what they are, how they can function, what abilities they have, is up to you. Maybe make it some sort of "change of pace" game, where the characters are recognizable, but their capabilities are changed for the purpose of being in the prison. Ultimately, they have to break out of this prison.
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Make them prisoners of the rat realm or something truly twisted. An urban-type setting that is nothing but piles of bones, debris, and other teeming rats. They have diminished physical capabilities (being rats and all) but maintain their mental abilities.
As punishment for the looting, though, I would insist that their gear was gone. Might make them rethink wanting to keep the guys...