Perplexity is a game about what happens when the “shit hits the fan” on a distant world. A world on which human colonists have encroached into the territory of an alien species like they have never seen.
The prime directive of these colonists: To coexist in harmony with the ecosystem of their new world. However, none of them expected to encounter this new alien life. The scout ships have a screening system to detect semi-intelligent and intelligent life on worlds and remove them from the database of targets for colonization. Who knows how or why this failed, and while you may ponder, it is simply too late now to pack up and leave. The resources aren't present to abandon colonization, it is adapt or die. You must try and deal with this new threat to peaceful development, in a clear state of perplexity.