You can have multiple endings. The first is when Amos changes his ways, but you can't write anything down on his sign. The second is when Amos doesn't, and kills Stubs. The only difference, though, is that Luke looks at you when he sees Amos isn't there.
So, here's my perspective. Pete is in a coma, probably on life support and his sister is probably very close to Pete, but she might be dead. The final chamber with the egg sacs look like a brain, so that' his head, or brain, and when he's been takin off life support, he dies and goes flying and his mind is free to go to heaven. He hears his sister talking to him, so when he hears her say "I'll see you soon" that means he'll see her again after.
 "Epic Battle Fantasy 3"){kind=icon}
 "Arcuz - Behind the Dark"){kind=icon}
 "Reincarnation: Let The Evil Times Roll"){kind=icon}
 "PixEvo - The Fountain"){kind=icon}
 "Heir"){kind=icon}
 "The Wizard's Notebook"){kind=icon}
 "Epic Coaster"){kind=icon}
 "Harry Quantum: TV Go Home"){kind=icon}
 "Solipskier"){kind=icon}
 "Hanna in a Choppa"){kind=icon}
 "Coma"){kind=icon}
 "Anti-Idle: The Game"){kind=icon}
 "Epic War 4"){kind=icon}
 "Final Ninja"){kind=icon}
 "Billy's Big Adventure 3: RPG Edition"){kind=icon}
 "MARDEK RPG: Chapter 3"){kind=icon}
 "MARDEK RPG: Chapter 2"){kind=icon}