"Manitou is deep within Mother Earth, in a place where the voice of Father Sun cannot reach. Stealing away all life from humans in this land... Man and Manitou... One must perish... They cannot both live in harmony."
Manitou refers to the concept of a Great Spirit or of the interconnection and balance of nature or life in many Algonqiuan Native American groups, similar to the concept of Brahman in Hinduism.
While Manitou itself is based on the concept of a spirit inhabiting all things - not only people and animals, but plants, stones, and even machines - the villain itself appears to be based on the "Otshee Manitou" or bad half of the spirit, while Nemissa appears to be based on the "Aashaa Manitou" or good half. Manitou, in Algonquian, has been translated as either "spirit" or "god."
Graham Masterton's Manitou series (starting with a book-turned-movie called The Manitou) may have had some influence on Soul Hacker's Manitou, as the method in which the book's villain appears is loosely mirrored in Soul Hacker's final confrontations: indirectly facing a shaman, beingreborn through a host, tumor-like growths, and inevitable possession.
Originally Manitou was a great spirit of the land found in North America, but Kinap utilized Manitou as a weapon in ancient times. Contact with mankind and their souls threatened to turn the peaceful mindless force into an entity of destruction. Kinap then sealed Manitou away and created Nemissa from Manitou to bring death to it should it ever be awakened and become a force of destruction.
The Phantom Society and Kadokura find the entity, and make their own plans to give it the souls of mankind for their own agendas. Manitou is also capable of feeding on the souls of demons, as shown by the slain Godly soul that it gains power from.
Kadokura's original goal is unknown, as he simply seeks to feed the souls of humans to Manitou and was insane. Manitou was also key in the Phantom Society's goal of harvesting souls via the Krypto Chip, as he is the parent body in the soul accumulation process. The Manitou Net was installed the Nikamimon Ruins, after Naomi cleared out one of the troublesomedeities still slumbering down there during the early years of the project. The slain god's power would later be absorbed by Manitou.
He is the last boss, fought in Powerstone Hall when Kadokura fuses with him. Initially appearance as a giant stone object surrounded by glowing blue light, it transforms Kadokura and creates a golden humanoid form to fight. After beating him, he cries out in sadness. Only Nemissa understands him, saying that he wants to die. She says she understands her reason to exist, and tells the protagonist that it's been fun. With this, she leaves Hitomi's body, returning to Manitou. Manitou falls silent, then begins to disappear from the human world.
If Naomi defeated Tiamat, the protagonist will fight this form. At half health, it'll remove all buffs on party and debuffs on itself, and switch to more dangerous magic. At low health, he begins to attack twice per turn.
If Naomi defeated Apsu, the protagonist will fight this form. Physical attacks inflict splash damage in this form. When his health gets low, he will begin to use Second Sun and attacks twice per turn. Second Sun only strikes those in positions 1, 3, and 5, so it is best to keep sturdy demons that in those positions.