Well, a plot twist seems like a good idea to me. But how about this:
In the end it turn out that the only reason the players were send on that mission was because they wanted to get rid of them. or at least to keep you busy for a while.
They won't discover that until the end.
However, in the end the mission seemed to be useful after all. Maybe because the player has discovered something important or destroyed something witch would have caused a lot of trouble if it was not destroyed on time.
Just throwing some ideas here. Perhaps it might help you. ;)