Team partners Haruhiko Ichijo and Mai Kawakami hunt down a Fire Phantom wreaking havoc at the high school division of their prestigious private school Hosea Academy, but Arisu Himeno, their supervisor of the Phantom-hunting Club in the Neural Error Corrections Room, confiscates their reward since they caused damage to the high school clock statue. Wandering into a cemetery, Haruhiko witnesses Reina Izumi using her special ability to consume Cemetery Phantoms. Fascinated by this, Haruhiko tries to recruit Reina on his team in the Phantom-hunting Club, though she initially refuses. After Haruhiko treats Reina to lunch in the high school cafeteria, he explains that the Alayashiki Company's research facility was hit by a terrorist bomb over a decade ago, releasing a virus that infected the human brain. This caused changes in brain function, resulting in everyone being able to see Phantoms, which are any ghosts, yōkai, monsters and other supernatural beings. Moreover, children born after the incident were given special abilities genetically designed to fight Phantoms. Those with special abilities established club-like groups within their schools in order to seal and expunge troublesome Phantoms for a reward. After Haruhiko introduces Reina to Mai, the three of them set off to deal with wooden Utility Pole Phantoms called Tsukumogamis, which are causing radio disturbances. Reina successfully seals the Tsukumogamis after Mai competes with them in a traditional game of limbo.

Haruhiko wants to be more valuable to his team by learning how to summon Phantoms using his sketchbook. Arisu assigns Haruhiko, Mai and Reina to assist Koito Minase, a newly transferred student who first manifested her special ability of her singing voice at a young age. They are requested to go to the Alayashiki Company's abandoned factory, where there have been reports of a Security Robot Phantom causing a disturbance by controlling drones. Since the Security Robot Phantom uses antiphase sound waves to cancel out Koito's singing voice, Haruhiko, Mai, Reina and Koito work together to seal the Security Robot Phantom. While Mai and Reina cool off at Haruhiko's house, Haruhiko's Fairy Phantom named Ruru reveals that she found a mysterious gadget at the abandoned factory. The next day, Haruhiko tells Mai and Reina that a Parole is a unique spell used by special ability users. Arisu soon assigns Haruhiko, Mai and Reina to deal with a strange UFO Phantom that peeps on the college girls in their dormitory. While Mai and Reina lure the UFO Phantom by wearing towels, Haruhiko eventually implements his Parole by summoning a sketch of Marchosias using a cut on his finger. Although appearing as a winged puppy, Marchosias still manages to capture the UFO Phantom, allowing Reina to seal the UFO Phantom. Reina heals Haruhiko's cut finger with her mouth. As Koito passes by, she is unimpressed by how Haruhiko, Mai and Reina handled the task.

Haruhiko, Mai and Reina meet up at the train station, where Mai recalls being a wallflower during childhood. They are tasked to deal with two female Bridge Phantoms who challenges people to a contest of strength. The Bridge Phantoms are specifically seeking to fight Mai, but she quickly loses against them. Haruhiko summons Marchosias as a distraction for a tactical retreat. The next day, Mai attempts to train Haruhiko and Reina in combat. Haruhiko then suggests for Mai to copy her semantic memory, episodic memory and procedural memory into his brain without the need to train in combat. With Arisu's help, Haruhiko and Mai visit an amusement park, a movie theater and a climbing gym among other places in order to synchronize shared memories, though Reina expresses jealousy. Heading back to the bridge, Haruhiko and Mai are challenged to a fight by the Bridge Phantoms. Haruhiko and Mai end up synchronizing shared memories, to which Haruhiko realizes that the Bridge Phantoms are actually two girls whom Mai befriended during her preschool field trip ten years ago. Believing that Mai was rather extroverted instead of introverted, Haruhiko concludes that Mai altered her memories. Since Haruhiko lacks the stamina needed to fight, Arisu suggests for Haruhiko to implement Mai's special ability. Haruhiko and Mai perform a simultaneous attack using Mai's special ability of the five elements against the Bridge Phantoms, who finally vanish after accepting defeat. The next day, Arisu suspects that Mai's memories will vanish from Haruhiko's brain within a few days, while Reina wonders if she will ever become closer to Haruhiko and Mai.

Haruhiko, Mai and Reina go to an all-you-can-eat restaurant, where Reina proves her large appetite. At sunset, Reina boards a mysterious red bus on her way home. The next day, Koito confirms that the red bus is actually a Bus Phantom that has possessed Reina. At the next sunset, Mai and Koito watch as Haruhiko and Reina board the Bus Phantom before it disappears. Haruhiko and Reina find themselves in a fantasy house, where Reina is entranced by two Bunny Phantoms acting as her perfect parents at the dining table, while Haruhiko is believed to be Reina's older brother. Waking up outside Reina's house, Haruhiko and Reina realize that almost no time has passed since they boarded the red bus. The following day, Koito explains that the Bus Phantom hypnotizes victims by using food and takes over their consciousness. Reina says that her older sister ran away from home because her strict parents despise Phantoms. At the following sunset, Haruhiko, Mai and Reina board the Bus Phantom, finding themselves in the same fantasy house, in which Mai is believed to be Reina's older sister. Entering the bathroom as a way to snap out of it, Haruhiko manages to help Reina come to her senses. Reina is nearly persuaded by the Bunny Phantoms offering her to stay in the fantasy house. However, she chooses to abandon the fantasy house when Haruhiko reveals that he is still waiting for his mother to come home. The next day, Haruhiko and Mai learn that Reina came clean to her parents and received permission to stay in the Phantom-hunting Club.

Koito uses her special ability in order to seal a Train Phantom. She notes that she keeps her distance from people ever since her special ability surfaced four years ago. During lunch, Haruhiko's friend Shosuke Morohashi says that Koito appears standoffish even though she used to be popular. Arisu assigns Koito to deal with a Dragon Phantom attacking the school chicken coops and rabbit hutches. Upon meeting Kurumi Kumamakura at the primary school division of Hosea Academy, Koito encounters the Dragon Phantom, but it renders her special ability useless. Just as Haruhiko, Mai and Reina arrive to help, Kurumi uses her special ability of transforming her inanimate teddy bear Albrecht into an animate fighting giant, causing the Dragon Phantom to flee. Arisu suggests a race to determine who will be the first to hunt down the Dragon Phantom. Mai, Reina and Kurumi form a team, while Haruhiko and Koito reluctantly form another team. Haruhiko and Koito are the first to find and confront the Dragon Phantom, but it flees once again. Arisu later tells Haruhiko that the Dragon Phantom awakened Koito's special ability four years ago. Stubbornly and solely facing the Dragon Phantom at the zoo, Koito is soon saved by the timely arrival of Haruhiko, Mai, Reina and Kurumi, who all combine their special abilities in order to seal the Dragon Phantom. Reina heals Koito's injuries with her mouth. Arisu reveals that the Dragon Phantom is different from the one that Koito encountered four years ago. At his house, Haruhiko tries to repair the mysterious gadget, and Koito waits outside in order to give her thanks and apologies to him before storming off.

Kurumi is afraid to disappoint the people who rely on her and would prefer not to be involved in fighting Phantoms. At a crosswalk, Kurumi encounters Haruhiko, as they are transported to a fantasy kingdom inhabited by sentient teddy bears. Kurumi is claimed to be their missing princess, while Albrecht appears as Kurumi's royal guard, defending her from the Higuman teddy bear soldiers in service to the evil prince Salmon de Higuman III. In his lair, Albrecht tells Haruhiko and Kurumi that Salmon plans to marry Kurumi after he took over the throne. Albrecht departs after returning a golden rake to Kurumi as her family heirloom. Haruhiko concludes that they are stranded in an alternate world created from Kurumi's memories centered around bears, including the animal itself, her favorite food, her birthplace and her surname. Albrecht arrives to report that Salmon is planning to attack with his vanguard. Meanwhile at the Neural Error Corrections Room, Koito tells Mai and Reina that Kurumi is capable of fighting but needs to get over her mental hangups. After Albrecht is shot with a bow and arrow, Haruhiko and Kurumi take Albrecht to the forest, where Kurumi remembers that Albrecht gave her the confidence to make new friends. When Salmon attacks with a giant robot teddy bear, Kurumi overcomes her fear and confronts Salmon by herself. Kurumi activates the golden rake, which transforms her into a magical girl, allowing her to easily defeat Salmon. Haruhiko and Kurumi then leave the fantasy kingdom and return to the crosswalk in the real world. Back at the Neural Error Corrections Room, Mai asks Kurumi to come along in order to deal with a Phantom, and Kurumi happily agrees to help.

At the high school, the students unknowingly begin behaving like cats, notably long naps and fish cravings. Mai explains that a nearby cat mansion was previously a dormitory, but it was closed down after it was overrun by stray cats. Kurumi asks Haruhiro, Mai and Reina to track down a missing kitten named Rudolph for her friend Arina. The next day, Mai, Reina, Koito and even Kurumi are among the students who show up to the high school with cat ears and cat tails, much to Haruhiko's shock. Haruhiko, Mai, Reina, Koito and Kurumi explore the cat mansion, where they eventually realize that they are inside a Cat Mansion Phantom, though Koito and Mai are each unable to seal the Cat Mansion Phantom. Thanks to Kurumi's plea, the Cat Mansion Phantom returns Rudolph, restores the cat mansion and reverts all the students back to normal. Kurumi explains that the Cat Mansion Phantom was lonely when the cat mansion was closed down and the stray cats went away. Before leaving, Haruhiko, Mai, Reina, Koito and Kurumi clean the cat mansion, while Arisu comes by to announce that the cat mansion will be turned into a tea house for the students.

Under the sweltering heat, the high school grounds have transformed into a hot spring guarded by an adult male Monkey Phantom. Several students including Shosuke, the Beach Angels, Mai, Haruhiko, Kurumi and Koito each fail in their attempt to seal the Monkey Phantom. Haruhiko and Mai then dress up as a pantomime horse and approach the hot spring, but their cover is easily blown. Later on, Haruhiko suggests for Reina, Kurumi and Koito to pose in their one-piece swimsuits as a way to lure the Monkey Phantom out of the hot spring, but the Monkey Phantom does not find the three of them attractive enough. As a last resort, Haruhiko paints Mai's buttocks red as a way to attract the Monkey Phantom. However, Mai accidentally spills red paint on Haruhiko's sketchbook, making Haruhiko unable to complete his sketch. Instead, Haruhiko summons Cthulhu, though appearing as a giant baby octopus, in order to capture the Monkey Phantom, allowing Koito to bind the Monkey Phantom. Ruru learns that the Monkey Phantom was abandoned by his wife and wanted to relax in the hot spring. A mock wedding is held in order to cheer up the Monkey Phantom, and Haruhiko plays the unfortunate role of the bride. The hot spring disappears as the Monkey Phantom departs from the high school with a reluctant Haruhiko in tow.

Ayumi Kitajima, the sole member of the Drama Club, eventually convinces Haruhiko, Mai, Reina, Ruru, Koito and Kurumi to participate in the regional competition for her play loosely based on the Ikedaya incident. Haruhiko, Reina, Ruru and Mai are respectively cast as Toshizo Hijikata, Soji Okita, Isami Kondo and the Phantom's hostage, while Kurumi and Koito are respectively cast as Ryoma Sakamoto and Izo Okada. Ayumi also casts herself as the Phantom. The rehearsals were arduous but gratifying. On the day of the regional competition, Haruhiko, Mai, Reina, Ruru, Koito and Kurumi begin their performance. In the middle of the play, Ayumi is revealed to be a Bakumatsu Phantom, who was manifested from the suppressed rage and frustration of losing the regional competition for ten straight years. Moreover, Ayumi pretended to be a sophomore drama student by manipulating the memories of the others. Instead of sealing Ayumi, the others decide to finish the play. Ayumi then transforms the stage into an illusion of the scenery around and inside Ikedaya Inn, while the audience members serve as extras. Haruhiko, Mai, Reina, Ruru, Koito and Kurumi follow the script, leading to a triumphant battle against Ayumi. The stage finally returns to normal, and they win the regional competition. The next day, Ayumi insists that the others can make it to the national competition with more intensive rehearsals throughout the entire summer vacation.

After Haruhiko accidentally steps on Ruru, she becomes tired of being small. At a park, Ruru meets a benevolent Witch Phantom, whose purpose is to grant the wishes of other Phantoms. As Ruru immediately wishes to be human-sized, the Witch Phantom transforms Ruru into a human girl and arranges for her to be in Haruhiko's class as a transfer student named Natsuno Ramune. The only catch is that Ruru cannot fly, and that she will go back to being fairy-sized if anyone finds out her true identity. Haruhiko soon introduces Natsuno to the Phantom-hunting Club, and Natsuno provides a believable sob story. Heading to the fireworks festival dressed in yukata, Natsuno feels guilty when Haruhiko, Mai, Reina, Koito, Kurumi and Arisu all desire for Ruru to be there with them. Meanwhile, the Witch Phantom finds a discarded Firework Phantom, granting his wish to go off with an unforgettable bang. During the fireworks festival, Haruhiko bandages Natsuno's sore feet while confiding in her that he wants Ruru to be there with him even though she is usually troublesome. The Firework Phantom crashes the fireworks festival, putting people at risk with his imminent explosion. As Koito, Reina, Mai and Kurumi are each unable to seal the Firework Phantom, Haruhiko ends up attached to the Firework Phantom. In order to regain her ability to fly, Natsuno reveals her true identity as Ruru, reverting to her fairy-sized self. The Firework Phantom releases Haruhiko into the river after Ruru convinces the Firework Phantom to explode higher in the sky with her. Ruru surprisingly reappears unharmed, and Haruhiko scolds Ruru for causing worry. As a display of fireworks explode in the sky, Haruhiko buys a bottle of ramune for Ruru and apologizes for stepping on her earlier.

With summer vacation right around the corner, Haruhiko, Mai, Reina, Koito and Kurumi have the highest grades compared to the other teams in the Phantom-hunting Club. Koito tells Haruhiko that he has been repairing a communication device for accessing the Alayashiki Company's servers. The next day, Arisu warns the students about an unidentified female Phantom named Enigma, who attacked three students from another school and stole their special abilities. Later on, the Beach Angels are attacked by Enigma, who steals their special abilities by kissing them. Haruhiko, Mai and Koito come to the rescue and attempt to seal Enigma, but she vanishes without a trace. Since the Beach Angels never regained their special abilities, it is deduced that Enigma is still on the run. While Haruhiko continues repairing the communication device, he receives a phone call from his mother to meet up at the playground. After they reconcile, Haruhiko's mother agrees to live with Haruhiko again. One week later, Mai, Reina, Koito and Kurumi deal with a Sunflower Phantom. After spying on Haruhiko and his mother at a grocery store, Koito tells Mai, Reina and Kurumi that Haruhiko's mother might be a Phantom. Mai, Reina, Koito and Kurumi visit Haruhiko's house for dinner. Haruhiko's mother embarrasses Haruhiko by sending her blessing for the girls to marry him. Mai is contacted by Arisu, who informs that Haruhiko's mother has been reported missing for a week. Suddenly, Mai is attacked by Haruhiko's mother, revealing that she is possessed by Enigma. The girls helplessly watch as Enigma steals Haruhiko's special ability by kissing him before she leaves the unconscious body of Haruhiko's mother and flees. To make matters worse, Haruhiko and Ruru simultaneously fall unconscious, much to the worry of the girls.

The students of Hosea Academy take a summer trip to a seaside resort. Haruhiko expresses that he hates summer, and he would rather stay indoors and read books. The boys point out that the girls will be wearing their bikinis. Upon arrival, the innkeeper explains that a Sea Monster Phantom scares away visitors every summer. Arisu then says that the rooms and meals will be complimentary if the Sea Monster Phantom is sealed. With no sign of the Sea Monster Phantom, the students enjoy their time at the seaside resort. Under the moonlight on the balcony, Ruru interrupts a potential bonding moment between Haruhiko and Mai. Reina, Koito and Kurumi join them while sharing dango. The next day, the students have fun in the sea. The Sea Monster Phantom appears and emits a mist at the students, creating an optical illusion of nudity with a polka dot phenomenon. Despite their efforts of modesty, the students fail in their attempt to seal the Sea Monster Phantom. When Haruhiko summons Marchosias and Chtulu in order to repel the effect of the polka dot phenomenon, the Sea Monster Phantom gets angry and emits a mist again, creating another optical illusion of nudity with white censor bars this time. After Haruhiko figures out that the Sea Monster Phantom can adjust the air temperature to change the refractivity, Koito, Mai, Kurumi and Reina each use their special abilities to trap, attack, capture and seal the Sea Monster Phantom. As the students can finally enjoy summer vacation, Haruhiko makes it back to shore after being swept by the wind waves caused by the girls. He returns without wearing his swim trunks, now actually nude instead of an optical illusion. Mai, Reina, Koito and Kurumi run away in embarrassment, while Haruhiko loudly expresses that he hates summer, even though Ruru likes it.