Pilot is Moya’s control centre--biologically and psychically bound to the leviathan--all of her systems are monitored and maintained by him. He is her major domo, keeping her functioning in top form, communicating for her, worrying for her so that she doesn’t have to--and he is rather a worrier.
Pilot was once a self-sustained individual, but now his upper-torso fused (more or less permanently) to floor and walls of his Chamber deep within Moya (which he obviously can never leave). He is part of Moya, even though he is very much his own species. He operates symbiotically with Moya. 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.
When D'Argo, Rygel and Zhaan chopped off his arm in a despicable trade agreement, Pilot was able to regenerate it. But the unpredictable nature of the conspirators in this event, have made Pilot and Moya acutely aware that the crew can never be entirely trusted. Despite this, and due to a bizarre, torturous experiment, Aeryn shares some of Pilot's DNA. This has given the warrior and the explorer a special affinity and a growing affection.