The setting stands in stark contrast to Earthbound until the game begins to disseminate small, ominous details that directly and indirectly reference elements and characters from the previous game with increasing frequency. Then it all culminates in Chapter 7's amazing series climax with Pokey. It's an unusually grim and particularly well-earned instance of fan service. There's even a fun boat ride.
Dead Space 2 is the obvious answer, amazing section of the game.
My other choice would be Resident Evil
Zero
Seeing the factory section from RE2 again with such nice graphics was amazing, even if it makes absolutely no sense whatsoever. Back then it really had me thinking we would be seeing REmake 2 sooner rather than so much later.
It's almost like it's a series about time travel where such things can and are reverted all the time (like everyone --literally everyone on earth-- dying in 1999 A.D. in the first game).