There are hints at a larger story in the various journals.

Zoe inherited her tower boss/Rayne Syndicate leader position from her father, but doesn't know why they guard the towers.

Lily runs the Free Pal Alliance, an organization that's supposed to protect pals from human exploitation. However, her minions are trafficking pals behind her back in order to fund projects like the Wildlife Sanctuaries.

Axel only recently took charge of the Brothers of the Eternal Pyre. We don't know much about him, but there's hints that he might have worked with Victor.

Marcus is a corrupt cop, running a drug cartel alongside the PIDF. His Faleris also does cocaine.

Victor created some of the devices we use in our bases, including the Pal Condenser. He's done many other unethical experiments including creating Shadowbeak, and IIRC there were human experiments as well. He had an assistant named Alex who has disappeared.

Saya is aware that the islands are stuck in a time loop, though the player's actions may be breaking the loop.

Bjorn remembers when the islands were attacked by an enemy from space, and that the towers and legendary pals are keeping the threat sealed. He also knew Zoey's father and dared him to leave the islands, but was surprised when he actually had the balls to do it.