After John escaped the Gammak Base with the help of his friends. Scorpius would have no doubt have looked into the history of each of the escaped prisoners, as well as Aeryn's history, investigating avenues that can be exploited in some way in the future.
He would have read that D'Argo was arrested by Macton, and if Jothee was turned into Macton by a sympathizer and enslaved because of his hybrid status. He could have a possible location to the boy.
Having Stark in his tender loving care for 2 years, he may have gleaned some name of a person or planet that Stark might visit to gain provisions. Scorpius could have leaked the location of Jothee in order for Stark to lead D'Argo and the others to the information. Also setting out wanted beacons to herd them in the right direction.
Not necessarily setting up the situation at the Shadow Depository, since he was surprised to realize that his belongings were taken by Moya's crew, but to set them up to capture at the auctions. Things became escalated quickly and he took the opportunity when it presented itself.