To go with the latest poll, here's a description of some of our potential bad guys.
Mermaid Terrorists: An anti-human faction of the Sisterhood that's afraid of more trouble from humans meddling in Atlantis.
Captain Nemo: specifically, Nemo II the one time sea going villain from Cryptida. He's got a personal grudge against Team Gernsbeck.
An Anutrofho Possessed Zombie : When Anutrofho was released the first time, she attacked several crewman of a pirate ship before destroying it. Her power might still be animating their corpses.
Dinosaur Smugglers: Because, what the hell?
Sorceress of Zoom: She is a collector of powerful magical artifacts, and the Library and the magic that powers the dome over the city might be quite tempting for her.