From the introduction:
Due to an incident in the gateroom, the PCs are going to discover they and they alone can see evidence of an alien “skin infection” amongst SGC personnel. The infected (which includes General Hammond) are displaying some odd behaviour and may be under alien influence. The source of the infection is SG-31 and one member of SG-16, recently returned from a world devastated by the Replicators. The players should try to contain the infection on the SGC, and will discover that it is caused by nanites. The nanites are designed for use with genetically engineered animals to create “programmed caretakers” for an alien city. In the absence of any animal life with sufficient smarts to get their creators’ civilisation up and running again, the nanites are “reprogramming” people to assist in a rebuilding programme on the planet.