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For the items concerned with the sewer pipes, you have to click the pipes in the right order. Simply having the items in your possession when doing so is enough, you don't have to do anything with the items themselves.
For the Power Cell, again you don't have to do anything with the thing itself. If you click on the "pods" with the Cell in your inventory, it is automatically used.
And no, if you exit Irenicus' Dungeon there is no way back. You can't access it later in the game.
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