Originally Posted by
The Tatterdemalion King
Try this instead:
Instead of the sabotage originating among the surface population (a population which is implied to be technologically unsophisticated or construction-resource poor anyway, hence the Federation assistance) it comes from an undersea population threatened by the dewaterfication project. They are the descendants of those who, 400 years ago, were genetically modified to live comfortably in the planet's new oceanic environment. The existence of the undersea civilisation is a secret the surface-dwellers are actively trying to obscure from the Federation, so it would make sense for the Crew to be members of the scientific advisory team instead of security.
I also suggest making the dewaterfication project way bigger and more cinematic in scale, like a surface-to-ice-asteroid mass transporter or a terraforming project to drop the planetary temperature into a new ice age (presumably what they had before). That would make the PCs potentially unknowing accessories to genocide.