In my story, a colony ship has made landfall on a planet. At first there is not thought to be any sentient life there, but after a while it becomes apparent that this is not the case.
The idea I have for the alien life form is that it can reproduce in a number of different ways - asexually, sexually, and by a process of transmittance. After a while the colonisers notice that a lot of the native plant and animal life shares specific alleles. This is from the sentient alien. It works by hybridising with other species, and this aids its own species survival by making once hostile organisms placid. (Like Toxoplasmosis in cats).
It's pivotal to the story that the aliens can breed with the humans, though this doesn't necessarily have to happen by a process of sexual intercourse. The parasitic DNA affects its host with new ways to communicate, a deeper sensitivity to other life. When mixed with humans, and everything that comes with it - anxieties, ambitions, politics - it provides them with communication capabilities that can’t be tolerated in a society that is just starting, and wants to retain what makes it human.
The aliens are driven back, as their main protection was the ability to conscript other species to its side, and aside from that they are essentially defenceless. All biology with a trace of this DNA is destroyed, until the land around is sparse.
But I need some actual biological explanation for it happening. This doesn't necessarily need to be hard science - after all, what I'm describing doesn't happen in the real world (I don't think). But I need there to be a sufficient amount of scientific explanation for the on board geneticist to hazard a guess as to how this has happened. In a later installment of the story, 200 years after the initial colonisation, I'd like to delve into the explanation a lot more.