Neo Ark is an underground location in Parasite Eve II. It is a converted shelter underneath Dryfield created by the Ark Shadow Government. It is now a secret laboratory that created the Artificial Neo-Mitochondrial Creatures. It is accessed through the abandoned mine.

In the Neo Ark, scientists created various types of AMNCs based on various environments on Earth, such the ocean, forest, and desert. They also created the GOLEM defense units. The lab houses various recreated environments to test their ANMCs in, but most of the lab is broken down and falling apart. This allows the ANMCs to roam throughout the shelter unhindered. The lab still has defense mechanisms running and Aya Brea confronts those as well as the AMNCs and the GOLEM defense units.

In the lab, there are notes of what the lab personnel had been experimenting with various organisms. There are various rooms in the shelter, such as the Breeding Room, and the Garbage Disposal Room. The Pupa NMC is fought here. The final battle takes place in Neo Ark.

Another major location is another level that is a massive greenhouse structure that is to provide a natural life for the ANMCs to evolve after being created. There are a lot of different environments, Savanna, Forest and water areas to name a few. There are also two massive Generators that provide power for the barrier that protects the innermost sanctum of Neo Ark, hiding the controller of these weapons: the new Eve.