When the Earth realizes that humans have become cancerous, it creates beings called the Agaro to destroy and replace humanity. In the years following their initial onslaught, Doctor June Lavolier created a floating city called Skytropolis that acts as a protective fortress and an ark in the event of an extinction level event. When the ghouls attack this stronghold, Doctor Lavolier's children, Malcolm and Nefertiti, along with her nephew, Dante, are donned in suits that turn them into the defenders of humanity's last bastion. However, when a secret about their lives is reveal, will it tear their family apart and destroy whatever hope mankind has for staying alive?
As the Paladins struggle to handle the revelation about their fathers and themselves, their relationship with their mother/aunt grows unstable as she distances herself from the children. Elsewhere, the Agaro continue their assault on the human race and further their agenda to reclaim the planet. However, are they the only threat the teen heroes of Skytropolis have to worry about?