Put simply, Pilot is a Pilot who has the job of being a Pilot. Sounds simple, but there is a lot more to him than meets the eye.
Little or nothing is known about Pilot's origins, but he dreamt of nothing but one day being bonded to a Leviathan and seeing the stars, as is thought to be the wish of most Pilots. And it is one wish that a Peacekeeper Lieutenant Velorik used to his advantage.
Velorik came to Pilot's homeworld when Pilot was relatively young for a Pilot. The elders had judged him not yet worthy of the sacred bond of a Pilot and Leviathan, and not capable of handling the responsibility. However, Velorik offered him a ship, offering to swap the current Pilot for him. Even though Pilot knew that the current Pilot would die, he was assured by Velorik that that Pilot would die anyway. Disobeying the elders, he left with Velorik to be bonded to Moya.
On board Moya, before the bonding process, Velorik usually acted kindly towards Pilot - they both had a mutual goal. But Velorik often administered discipline whenever captain Crais was around, in order to appear more responsible and capable. Shortly after, Pilot was bonded with the Leviathan, but it was not natural bonding but a forced bonding that was tortured into Moya, leaving Pilot in pain that the forced bonding would not allow to go away.
Moya was a prisoner transport for the Peacekeepers essentially, and Pilot's basic tasks involved guiding her through space and using the DRDs as labourers aboard. That is until Moya was liberated from her control collar by escaping prisoners aboard and Starbursted to freedom. Since then, Pilot has helped the escaped prisoners whenever possible, he and Moya not wanting to return to Peacekeeper servitude.
While Pilot's body is essentially Moya's, and vice-versa, both Pilot and Moya only control both those bodies, and not what the Peacekeepers have added, such as tracking devices. It was one of these, a Paddack beacon, and the ensuing events that caused Moya great harm. Pilot felt guilty for not knowing about it, caring for Moya's safety above all else.
However, painful events involving the past with the Peacekeepers made Pilot regret ever taking the place of Moya's original Pilot, and he ripped out his bonds to Moya. The crew managed to convince him to reconnect himself, and Pilot has started a natural, painless bond with Moya which could take a cycle to complete.
While Pilot cares about the crew of Moya, he cares about Moya first and foremost, and will carry out her instructions to the letter no matter what, although sometimes he can have doubts. He also does hold a slight grudge against some of the crew members for ripping off one of his arms in order to gain map-fibres to their home planets, which turned out to be fake. The same incident lead to Aeryn inadvertantly gaining some of Pilot's DNA through surgery, and she has also gained some Pilot mentality and understands the control system in Pilot's den.
Pilot does occasionally have arguments with the crew when their decisions conflict with his and Moya's, or if it possibly puts Moya in danger. But at heart he is kind and sensitive, using whatever DRDs are available at the time to perform tasks for them.
While Pilot does essentially have a heart of gold, he does have doubts about the other crew members, played on particularly by Traltixx, where he fathomed that he couldn't trust any of the crew members and he and Moya would be better off without them. In the end Traltixx was killed and Pilot regained his faculties.
One of the most important crew members, Pilot is rarely mentioned, although his role is significant. However, his job is a singular one that nobody else aboard Moya could possibly do, and in such a way he is quite isolated from the rest of the crew. Even so, he is reliable and can be trusted in every way by every member of the crew.