The party are part of a secret US government agency tasked with studying / protecting a cache of alien weapons and technology discovered in a cave in the New Mexico badlands. Thanks to a rosetta stone of sorts found in the Roswell crash, some of the text accompanying the find is translated. Phrases such as "extinction" and "the infestation" and "designed to exterminate the horrible creatures" and "protect the colonies" lead the group the belief that the alien weapons were designed to fight off some sort of invading horde.
They'll have to fight off other black ops agencies from other countries, and even some in the US government, that have also made similar discoveries and either want to be the only ones controlling the weapons or to force public disclosure. Eventually, they're authorized to use the weapons against other enemy agencies, to viciously deadly effect.
And then a hologram is unlocked. Even without understanding the aliens' spoken language, the images displayed are enough to explain that the infestation ... is man.