Pilot is an independent entity, but he operates symbiotically with his Leviathan (Moya), and the upper half of his torso, the part that we see, is the only part of him that is entirely his own. His much larger lower half is made up of neural tentacles which thread through and fuse with Moya's systems. Pilot is, to Moya, some combination of operator, bodyguard and partner. Because of this symbiotic fusing, he knows when she's scared, eager, excited, or sad, and he communicates Moya's thoughts to Crichton and the others. He and Moya are made complete by their ability to serve the members of the crew, but they are in no way obligated to follow the desires or needs of the crew if their own agendas disagree. Pilot is most often polite and respectful to the crew of Moya, but it's clear that his loyalty is to Moya first and the others second.