Best story in a Nintendo developed game

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Alkibiádēs said:

Metroid Prime 2 for sure, no Nintendo game has a better atmosphere or back-story. A truly under-rated gem. Read some of those scan logs and tell me I'm wrong lol.

In terms of atmosphere there are few games I have ever experienced that can rival Prime 2. It's still my least fav of the trilogy due to some gameplay quibbles, but its still an outstanding game.