Consider the possibility that Jool is a new villain.
In the first episode of Season 1, John accidentally killed Crais's brother, and Crais chased him across the galaxy for a year, until he and Crichton were both cornered on Scorpius's Gammak Nase.
In the first episode of Season 3, Stark accidentally kills Jool's cousin for John's benefit, and she will probably chase him across the galaxy, only to be cornered somehow on Scorpius's NEW Gammak Base.