Indeed (for the umpteenth time) Skullius knew that Serenity was hiding a lot from him. She didn't hide the fact that there was a lot she wouldn't or couldn't tell Skullius for one reason or the other.
So far, an earlier confrontation had revealed to Skullius that Serenity had wanted to flee to another reality and establish herself there. As Serenity wasn't allowed to have a bearer of her Null Life in this one, she wanted to do it in another reality, where she would have all the freedom she could ever desire.
To do this, she had employed the help of VOW to try and smuggle the Books of Alignment reserved for her future bearer, but the plan had fallen through, and in a desperate gamble, VOW made it so that Skullius became a Null Life bearer, even that ended up granting Serenity a punishment.
All this Skullius understood, but there was something Serenity had said in her explanation that had him thinking: