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When the Zion ship captains meet within the Matrix for the Crisis Meeting, Gnosis crew members Corrupt and Wurm are assigned to guard the door to the meeting place. When Smith arrives "looking for Neo", Corrupt speaks with him. Both Corrupt and Wurm warn the captains of the arrival of "the Feds", a trio of Matrix Agents.
When the Nebuchadnezzar returns to Zion, Neo is worshiped by some residents who believe he has the power to save them (he is clearly not comfortable with this). One elderly woman asks him to watch over her son, Jacob, who serves aboard the Gnosis.
The name of the Gnosis derives from the Greek word "gnosis", meaning knowledge.