I liked the one in Albion, a really really old RPG, where you'd crash land from your mothership onto an alien planet, believing it to be a completely barren wasteland and then finding it to be teeming with life.
You figure out beforehand that the corporation you're working for is evil, naturally, but you still need to find your way back to the mothership, and you spend almost all of the game exploring this new planet trying to find it.
You eventually find it in the middle of a desert. You're taken back on board, try to tell the crew what had just happened, and they all call you mad, because you're in the middle of a desert, so the rest of the planet must, as they have been told, also be a desert.
If I could have leapt into the game there and punched the captain in the face, I would have done.