Complex sentence: All Zion hovercraft crewmembers know that, upon encountering one, they should simply run away and try to escape, not only from the Agent, but from all nearby humans who could be potential hosts.
Split into simpler sentences: All Zion hovercraft crewmembers know that, and upon encountering one, they should simply run away and try to escape. But not only from the Agent itself, but also away from all nearby humans who could be potential hosts.