High schooler Momo Ayase, who comes from a family of spirit mediums, believes firmly in ghosts but denies the existence of aliens. Her classmate Ken Takakura, a meek occult enthusiast whom Momo nicknames Okarun, holds the opposite view, believing in aliens but not ghosts. To settle their disagreement, they make a bet that leads them to visit locations tied to both phenomena. Momo heads to a site rumored for UFO sightings, while Okarun explores a haunted tunnel. Their separate investigations prove that both the extraterrestrial and the supernatural are terrifyingly real.

At the tunnel, Okarun encounters a malevolent yokai known as Turbo Granny, who curses him and steals his genitals. Simultaneously, Momo is abducted by a group of aliens called the Serpoians, who intend to harvest her reproductive organs. In her struggle against the aliens, Momo awakens latent psychokinetic powers that allow her to manipulate objects. Turbo Granny, possessing Okarun, travels through the students mobile phones to attack the aliens, and the pair manage to fight back by combining Momo's psychic abilities with the supernatural speed and transformation powers Okarun gains from the curse.

After their ordeal, Momo brings Okarun to her grandmother Seiko Ayase, a surprisingly young and powerful spirit medium. Seiko expels Turbo Granny's consciousness from Okarun and seals it into a Maneki Neko cat doll, though Okarun retains the yokai's powers. However, Okarun's stolen genitals are now transformed into two golden balls of immense spiritual energy, and finding them becomes a central quest. The first golden ball is discovered by Aira Shiratori, a vain and popular fellow student who gains the ability to see spirits and believes she is a chosen hero destined to save the world. Aira initially views Momo as a demon, but after a confrontation involving the tragic spirit of a woman known as Acrobatic Silky, Aira inherits the spirit's powers and joins the group.

The story is set in the fictional Kamigoe City in Japan, a place where a small portion of the population is aware of the supernatural forces that reside or visit there. Seiko Ayase can borrow power from a local god to cast protective barriers, but these abilities are limited to the city's boundaries. As the series progresses, Momo and Okarun are joined by Jin Enjoji, nicknamed Jiji, Momo's handsome childhood friend and first love who comes to stay with the Ayase family. Jiji's house is afflicted by a powerful entity called the Evil Eye, which eventually possesses him, creating new challenges for the group as they seek a way to control or remove the spirit.

Throughout the first two seasons, the group battles a variety of supernatural and extraterrestrial threats. Okarun theorizes that aliens cannot defeat yokai, suggesting that Earth's mythological creatures act as a defense against alien invasion. This explains why aliens like the Serpoians seek to capture and experiment on humans who can acquire supernatural powers. Notable arcs include the search for Okarun's golden balls, the introduction of Aira and her Acrobatic Silky powers, Jiji's possession by the Evil Eye, and a confrontation with a space kaiju that leads to the reconstruction of Seiko's house using alien nanotechnology, which can be reconfigured into a giant Buddha-shaped mecha for battle. The first season ends on a cliffhanger with Momo in peril inside Jiji's cursed house, while the second season concludes with the revelation that the rampaging space kaiju is actually a suit worn by an alien girl.