The Pilot prior to Moya's original Pilot had been bonded to Moya for 21 cycles before she was killed at Peacekeeper hands.
In her time with Moya, Moya was being used as a Peacekeeper prison transport, frequently restrained by a control collar. At that point, Zhaan, Rygel and D'Argo were aboard Moya, even though the Pilot did not, to the best of my current knowledge, come into contact with any of them.
However, Moya was to be used by captain Crais for another purpose - the breeding of a Leviathan-warship hybrid. It is assumed both Moya and her Pilot knew about this and refused, and the Pilot refused to cooperate with the Peacekeepers. Lieutenant Velorik, seemingly a specialist on Leviathan-Pilot bonding, was summoned from High Command to locate and bond a new Pilot for Moya, under the theory that Moya would do as the Peacekeepers wished, so long as a Pilot led her to do so.
A new Pilot was found, and Moya's Pilot was ordered to be killed by an impatient Crais, just as lieutenant Velorik was trying to make her see the folly of her ways.
Crais' plan didn't fully work though. Velorik, caring for Moya and wishing to protect her from the abomination of Crais' plan, sabotaged it with, and hence was arrested by Crais. His sabotage efforts were never found by the Peacekeepers though.
All this happened three cycles prior to Moya's crew finding a recording of the Pilot's execution, and discovering that one of the executioners was none other than Aeryn. D'Argo however accidentally smashed the shield that Velorik had put in place, his little work of sabotage, leading to the birth of the genetically-incorrect Talyn, the result of Crais' project.