Scorpius subverts everything.
If there’s one thing you know about his character, it’s that. It’s a recurring theme in his character throughout the series-- the motivating factor behind everything he does. But he doesn’t do it with force; he does it with charm and subtle manipulation. We see it first when he boards Captain Crais’s command carrier and manages to take control within a matter of days, just by TALKING to the crew. By this point Crais has become unstable and violent; the moment one of his men start to question his orders, he lashes out at them. So along comes Scorpius-- this civil, soft-spoken creature who politely suggests the kind of superior strategy that Crais has long since abandoned-- and it’s an easy sell. By the time he makes an official move to seize command, the crew is all too ready to support him. Even later on in the series, when he’s aboard Moya and they’re holding him at gun point most of the time, he eventually manages to earn a begrudging degree of trust. Here’s a man who has tortured them-- chased them across the Uncharted Territories-- effectively ruined their lives, and with a few acts of selflessness and vulnerability, he’s almost turned himself into an ALLY.
It’s a theme we even see in his personal relationships. Over the course of the series we get to meet two of Scorpius’s lovers-- Natira and Sikozu. Both are incredibly powerful women who submit to no one else. But Natira-- who we meet after years of intimacy with Scorpius-- is immediately deferential to him the moment he enters the room. Everything she does is done with the intention of pleasing him-- including attempting to KILL him, because “You wouldn’t have respected me otherwise.” (This is where we learn with a certainty that if he puts his hand on your throat, it means he LIKES you.)
With Sikozu, things are a little different. She’s grown accustomed to always being the smartest person in the room, so she’s noticeably thrown when Scorpius-- in his subtle, understated way-- repeatedly demonstrates his masterful intellect. And in the early days of their relationship, they’re EQUALS. He’s a brilliant strategist, yes-- but her scientific acumen is highly appealing to him, especially after she discovers a chemical means to refresh the contents of his cooling rods. The series ends with Scorpius and Sikozu on almost equal footing, living kinkily ever after aboard his new command carrier.
Fast forward to Peacekeeper Wars, which takes place some months later (two? maybe?). Sikozu has the following conversation with Aeryn:
Sikozu: When I first met Scorpius, I naturally assumed I was his superior. I have since learned that there is a reservoir to his abilities that continually overshadows my own.
Aeryn: Same with Crichton.
Sikozu: You view Crichton as your superior?
Aeryn: No, as my equal.
Scorpius has slowly asserted his dominance over Sikozu, and she’s accepted it. And though it breaks my heart that they’re unable to maintain more of the equality that we see in the series, I believe the writers hit the nail right on the head with that particular exchange. Scorpius is MANIPULATIVE-- he uses people. He doesn’t know how to form a relationship without some sort of agenda. So naturally, the moment a woman comes along who genuinely cares for him (as both Natira and Sikozu clearly do) he takes advantage.