So, we have quite a nasty, violent, terrorist cult here- they seized control of the ship and weren't above killing for their beliefs- Archer temporarily tricked them into believing they executed him- they even professed the belief that 'it doesn't matter how many heretics have to die' (and they wanted to use Archer's ship to accomplish that). The episode ends with the members of this cult witnessing the ruins of their homeworld because both factions decimated one another eight months before. But what do you think happened with them after that? We don't see them anymore, and I don't think Archer locked them in the brig for the rest of the trip, given their mission and their scarcity of resources. Did Archer simply set them free, to fend for themselves on their devastated homeworld? Did he hand them over to some authority? Something else?