After you have fought the Ninja and watched/skipped the cutscenes that followed, have a look around Otacon's lab. You should notice a purple Nintendo Gamecube and a Wavebird wireless controller on one of the desks. On the TV next to it the screen shows...
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1. After the battle with the ninja and talking with Hal Emmerich for the first time, search the labratory computers for a little Mario and Yoshi
figurines on top of a computer.
2.Once you find them go into first-person mode and aim your gun at yoshi....
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