Musashi was a computer hacker and probably used his computer skills to good use as he worked for the CIA. Due to his past involvement with the CIA and being known as a gaming expert, he was well looked upon by Fox Mulder, John Byers, Melvin Frohike, Richard Langly, Ivan Martinez, and Phoebe.
Request to eliminate Maitreya
After the death of Retro during the FPS game, Musashi was contacted by the programers behind the game to eliminate the threat within the system to allow players to experience the game the way it was made.
Very early during the game, he lived up to his reputation and easily passed the first level of play. He then skipped the second level and went looking for Maitreya, the rogue element that killed Retro. However, Musashi was no match for Maitreya: using a 14th-century broadsword, she cut off his hands and then his head. (TXF: "First Person Shooter")