Just like in the original game, before the boss battle with Psycho Mantis he'll read data from the players memory card. From the MGS save file he'll read how often you've saved and if you're careful around traps. After that he'll dive deeper and if he finds save files from some other games - namely Super Smash Bros Melee, Super Mario Sunshine, Legend of Zelda: The Wind Waker or Eternal Darkness - he'll recognize them and make a comment about it.
In the room where you fight Psycho Mantis there are three portraits in the back (they are featured in the pre-fight cutscene where he makes them laugh manically). The people on these portraits were all involved with the creation of the game:
Ryûhei Kitamura (cutscene director)
Hideo Kojima (director and creator of the series)
Denis Dyack (director)
Connection to Other Media
In Otacon's office you can find two small statues of Mario and Yoshi on a filing cabinet. They are classic Nintendo-exclusive characters created by Shigeru Miyamoto, and appear here as a sign of teamwork since even if Silicon Knights developed the game it was Nintendo themselves who wanted an MGS game on the GameCube. If you shoot the statues Yoshi will make his classic sound while Mario will give you the extra life sound from the NES game Super Mario Bros in addition to giving Snake a little health refill.
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