Scorpius bought the lot with D'Argo's son just before Moya arrived and demands Crichton in exchange for Jothee. They plan to buy help of the beings they encountered before to break into repository, for the stolen money. But this money turns out to be alive and eats the ship. Then Crichton makes the ultimate deal.
Did You Know?
Just before the crew burn Moya, Zhaan places her hands on Pilots head (to share his/Moya's pain), and tells him to ignite the vapour. We cut away to the start of the fire, when we cut back Zhaan is facing the other way, and only turns to Pilot when he cries out. See more
[in John's head
There are vast regions of your brain that are filled with nothing but... gibberish.
That would be high school.