Cave Story (InstanceTopic, 17)
From Compile Worlds
Cave Story is an epic adventure about two amnesic robots from the surface who traverse the caves of an unnamed floating island on their quest to stop The Doctor from causing havoc by releasing frenzied Mimigas upon the surface of the Earth. Unfortunately, Toroko dies. Even if you put all that effort in to get the best ending.
Oops, spoilers. Sorry about that!