The Nikamimon ruins is an ancient temple complex dedicated to the Mesopotamian creation gods Tiamat and Apsu. It was chosen by Kadokura as the site for the Manitou Net -- and by extension, Amami City -- to be built upon. The presence of the ancient demons in there became a hindrance, and so Nishi hired a freelance summoner named Naomi to eliminate one of the demons. Descending deep into the complex, Naomi proceeded onward to the targets past a fork in the road: the left hand path led to the goddess Tiamat, while the right hand path led to the god Apsu. Naomi manages to defeat the demon, but the ancient deity suffocates her as it dies. This choice would have a significant effect later, due to the slain demon's power getting absorbed by Manitou.
The protagonist heads there personally following the events at the Amami Monolith, when a strange foam from the Manitou Net begins to cover the skyscraper. Following a tip from Lunch's Father, they learn that the Spores in the Krypto Chip were being shipped from a building near the Monolith, and surmise that Manitou is somewhere near it. From there, an elevator leads down to the ruins proper. Retracing Naomi's steps, they proceed deeper into the temple complex, using the Wheel Key they obtained in the Monolith to open the way to Powerstone Hall.
Within the chamber, they discover Manitou, and Nemissa could hear the souls harvested through Paradigm X crying out. Approaching closer, they are stopped by Kadokura, who has begun to fuse with Manitou and demands the power of more souls. Upon defeating his warped form, he becomes absorbed into Manitou itself, which emerges to fight the protagonist and Nemissa in the final battle. Depending on whether Naomi battled Apsu or Tiamat, Manitou will have different properties: if Apsu was slain, Manitou will utilize strong physical attacks, whereas if Tiamat was slain, Manitou will use deadly magical attacks. Once Manitou is subdued, Nemissa emerges from Hitomi's body to fulfill her true destiny as the song of death, ending Manitou and releasing the captured souls.