I'm not sure about the theming or story but here is my idea for a dungeon:

-I was inspired by Sigmascape v1.0 (Savage), with players having to go into train cars and do mechanics for their role.

First Part:
-At the beginning, players will separate into role-specific paths. Everyone will have enemies to fight: Tanks will be hard hitting and require using cooldowns, Healers will be weaker but place DoTs, and DPS will have to AoE through a bunch of enemies.
-For the first boss fight, the tank and healer will be fighting the main boss, while the DPS fight their own mini-bosses. As the DPS defeat their mini-bosses, the main boss will revive them using chunks of its HP.

Second Part:
-The group will be scrambled: The tank and one DPS and the healer and the other DPS. The Tank group will have to AoE mobs, while the Healer group will have to fight a mini-boss in a room full of poison/DoT-stuff.
-For the second boss, everyone rejoins each other. The boss will summon adds that are designed for the roles in specific areas. Once a player is steps into these areas, the area will seal off, sealing you, the add, and whatever mechanic they have in. The tank add will do a spicy, room-wide AoE, the healer one will do a room-wide AoE DoT, and the DPS one will divide into multiple units who ignore aggro.

Third Part:
-The group will separate again. The Healer will start off fighting the main boss, while the tank and DPS will start out fighting mini-bosses. The main boss starts off weak but will get stronger as mini-bosses are defeated but will also loose chunks of HP as well. Once a player defeats all their mini-bosses, that player will join the main boss fight. The tank's mini-bosses will have less HP.