the desert town of Dryfield, Nevada, over reports of unusual animals. While initially displeased with the assignment, Aya learns from MIST's technical expert Pierce Carradine that an implant recovered from one of the new NMCs has desert sand unique to that area of Nevada near Dryfield. Aya arrives to find the tiny town overrun with NMCs and makes contact with Gary Douglas, a survivalist and gun enthusiast who is the sole remaining inhabitant of the town, his dog, Flint, and Kyle Madigan, a private investigator who claims he is on a mission similar to Aya's. He tells her about "The Shelter", a nearby underground facility that may hold the answers to the recent outbreak of NMCs. After spending some time in Dryfield and having another run-in with No. 9, Aya and Kyle are able to reach an entrance into the shelter within an abandoned mine. As Aya explores the shelter which has become overrun with NMCs she discovers numerous scientific facilities and learns that the shelter was created to enact the "Second Neoteny Plan", a project to deliberately create Artificial Neo-Mitochondrial Creatures (ANMCs, the new humanoid creatures) in the belief that they are superior to humanity. Aya also learns that the mutant mitochondria the ANMCs were created with is actually her own, and with the aid of Pierce learns that the shelter acquired her genetic material directly from Baldwin and MIST, which has secret ties to the conspiracy that founded the shelter. She also learns that the Second Neoteny Plan is nearing its culmination with a massive cocoon containing an ANMC that, when fully grown, will be able to generate a vector virus that will transform the entire human race into ANMCs. Haunted by visions of a mysterious girl and seeking to put an end to the threat from the shelter, Aya progresses into the Neo-Ark, a zoo-like artificial construction hidden deep in the shelter. Originally intended to be a showcase of ANMCs with multiple different habitats and viewing platforms, Neo-Ark was ground zero for the outbreak of creatures and has also been overrun by various kinds of NMCs. Aya is able to disable the two organic power generators to reach the depths of the shelter, and finds the mystery girl. After defeating her ANMC guardian, Aya is able to discover that the girl, Eve, was cloned from Aya's genetic material to be the final key to the Second Neoteny