Episode 1: Haruhiko Ichijo explains that due to a chemical accident by the Alayashiki Company changes were made to the brains of every human on earth allowing them to see and interact with Phantoms previously thought to only exist in stories, and many babies born after the accident are born with special abilities allowing them to fight Phantoms. Haruhiko and Mai Kawakami spend their days hunting down troublesome Phantoms by themselves in order to earn rewards from their school. However, their latest reward is confiscated after their battle with a Phantom caused damage to the school. Haruhiko witnesses Reina Izumi defeat a Phantom by consuming it and immediately asks her to join the Phantom Hunting Club. Though she initially refuses she later joins Haruhiko and Mai in dealing with telephone pole phantoms by defeating them in a limbo contest.
Episode 2: Haruhiko talks about how reality is merely how the brain perceives the world and how Phantoms are still not entirely understood. Haruhiko tries to become more useful by learning how to summon Phantoms and Demons using his sketchbook. Haruhiko, Mai and Reina are tasked to assist another Phantom Hunter, Koito Minase, who can seal Phantoms using only her voice. They are asked to take down security robots that have become Phantoms in an abandoned factory, where Haruhiko retrieves a mysterious device. On a later occasion, the team is asked to deal with a strange UFO-like Phantom that watches the girls dorms and takes photographs when they change their clothes. Haruhiko attempts to use his new skill to summon the Hellhound Marchosias, but it turns out to be a puppy with wings who nonetheless succeeds in capturing the UFO. Reina reveals she has a healing ability. Koito dismisses the team as useless and unimpressive.
Episode 3: Haruhiko talks about research being done into making human memory as accurate as a computer. Mai recalls her childhood as a shy cry-baby. They must deal with a Phantom on a bridge that challenges people to combat. The team are being watched by a young girl with a teddy bear. The Phantom is two sisters who insist on fighting Mai who quickly loses. Mai decides to train Haruhiko and Reina to fight alongside her but fails. Haruhiko suggests they copy Mai's memories into his brain so he can fight without having to train. Haruhiko and Mai go on a "date" to synchronize shared memories, of which Reina appears jealous. Mai recalls how she had two childhood friends, the only ones who would play with her. The two Phantoms reappear and fight Mai and Haruhiko who end up synchronizing memories. Now fully trained Haruhiko realizes the Phantoms are Mai's childhood friends, and Mai had reshaped her own memories. Rather than being shy she was actually very competitive and often beat the Phantoms in wrestling, who have now trained for 10 years to finally beat Mai. Haruhiko finds that while he now knows how to fight he lacks the athletic ability to actually be able to. Instead he uses Mai's memories to perform a synchronized magical attack with Mai, defeating the Phantoms who leave on good terms with Mai, promising to return for a rematch after more training. While Haruhiko thinks Mai's memories will eventually disappear for the time being he enjoys being able to remember Mai's bra size.
Episode 4: Haruhiko lectures on the similarities and differences of families across different cultures. Reina proves how large her appetite is at an all-you-can-eat buffet and later regrets she must return home to her strict parents, who hate Phantoms and do not know Reina is a Phantom Eater. She boards a strange bus. Haruhiko thinks Reina is being influenced by a Phantom. Koito confirms the bus is a Phantom and Reina is possessed. The next time Reina boards the bus Haruhiko joins her and finds himself in a fantasy world where Reina is entranced by rabbit Phantoms who give her a delusion of a perfect life with a nice family and Haruhiko, now a part of the fantasy, believes he is her older brother. They wake up outside Reina's house with virtually no time having passed since they boarded the bus. They realize Reina was targeted by the Phantom due to her unhappy home life. Next time Mai joins Haruhiko and Reina on the bus and comes to believe she is Reina's estranged older sister. Haruhiko escapes the fantasy and wakes up Reina, causing the Phantom to reveal itself. It offers to let Reina keep living the fantasy and she almost accepts until Haruhiko reveals he also has a sad home life but waits for the day his mother will come home. Reina decides to abandon the fantasy and so the Phantom is defeated. Back in the real world Reina tells her parents the truth and receives permission to stay in the club.
Episode 5: Haruhiko talks about how singing has a variety of benefits for the brain. Koito uses her singing ability to defeat a Train Phantom. She explains she has avoided people since her power appeared and usually fights Phantoms alone. She is asked to deal with a Phantom attacking school pets. Koito meets young student Kurumi Kumamakura and her teddy bear Albrecht who cares for the schools rabbit. The Phantom attacks and renders Koito unable to sing. Kurumi uses her power to transform Albrecht into a giant fighting version of himself to attack the Phantom which disappears. Koito insists on hunting the Phantom alone without help. They decide to make it a competition to see who catches the Phantom first with Haruhiko deciding to team with a reluctant Koito. Haruhiko and Koito find the Phantom first though it flees once again. Haruhiko discovers Koito blames the Phantom for ruining her life as it was the one that first caused her ability to manifest. Koito stubbornly faces the Phantom alone and is eventually saved by Haruhiko and the others who defeat the Phantom. Koito is healed by Reina. Their class teacher reveals that the Phantom was misidentified and is not the one Koito met as a child. The next day Haruhiko is still trying to repair the device from the warehouse and Koito appears outside his house to thank him for his help before storming off.
Episode 6: Haruhiko talks about young children and their attachments to dolls or blankets to feel safe. Kurumi is afraid to disappoint the people who rely on her and would prefer not to be involved in fighting Phantoms. She meets Haruhiko and the two are transported to an alternate world inhabited by Teddy Bears similar to Albrecht who claim Kurumi is their missing princess and Albrecht, her royal guard, defends her from other teddy bears in service to the evil Prince Salmon who stole the throne and plans to marry Princess Kurumi. Albrecht returns Kurumi's family heirloom, a golden rake. Haruhiko concludes that they are stranded in a Phantom space created from Kurumi's own memories. Prince Salmon attacks with his army. In the real world the girls are confident Kurumi is a capable fighter if only she can overcome her fear. Albrecht is hurt protecting Kurumi who remembers how it was Albrecht who gave her the confidence to make friends growing up. Prince Salmon attacks once more, this time with a giant robot bear. To protect her friends Kurumi overcomes her fear and battles Prince Salmon with her golden rake which transforms into the Golden Bear Hand with which she easily defeats Prince Salmon. After a tearful goodbye with Albrecht Kurumi and Haruhiko return to the real world. At the club Mai asks Kurumi for help dealing with a Phantom and Kurumi happily agrees to help.
Episode 7: Haruhiko explains the thought experiment Schrodinger's cat and how it relates to Quantum mechanics. Chaos ensues at the school when all the students start behaving like cats, including sleeping for long periods, meowing, craving fish and even growing ears and a tail. The team is asked to find a missing kitten which is tracked to a Phantom hiding in a mansion closed years before when it was overrun by cats. Once inside they realize the Phantom is the house itself possessed by a cat spirit who became lonely and angry when the mansion was closed and students from the school stopped visiting. After Kurumi pleads with the Phantom to return the kitten the Phantom is happy with how Kurumi loves the kitten and returns it, returns the mansion to normal and changes all the students back to normal. Before they leave they decide to clean the mansion and the school decides to turn the mansion into a tea house for the students.
Episode 8: Haruhiko talks about how humans have used hot springs for leisure and for the health benefits for thousands of years. A gang of Phantom Monkeys transform the school grounds into their own Hot Spring which is guarded by a large perverted Monkey Phantom so no one else can use it. Every attempt to defeat the Phantom fails and even Haruhiko is unable to seal the Phantom with his sketch book as he cannot see the Phantoms feet underwater and therefore cannot draw them. Attempts are made to lure the Phantom out of the water using girls in a variety of revealing outfits, but the Phantom isn't attracted to any of them. The Phantom is eventually lured out by Mai but Haruhiko spills paint on his sketchbook and is still unable to complete the drawing, instead summoning the octopus demon Cthulhu to trap the Phantom so Koito can sing it into submission. Before they finally defeat the Phantom, Haruhiko learns the Phantom was just upset that his wife had left him. To cheer him up they hold a fake wedding for the Phantom with Haruhiko playing the unfortunate role of the bride. The Phantom departs with Haruhiko in tow and the hot spring disappears.
Episode 9: Haruhiko starts with an explanation of why humans enjoy hearing stories about the past. Classmate Kitajima Ayumi from the Drama Club convinces Haruhiko and the others to take part in her play for the local competition. They begin rehearsals which they find quite demanding. On the night of the competition Kitajima, who is playing the evil Phantom, is revealed to be an actual Phantom born from the frustration of the school students who have been losing the competition every year for ten years and whose only desire is to finally win. The Phantom transforms the stage into the real setting of the play with even the audience members becoming part of the background. Following the story Haruhiko and the others battle the Phantom against the backdrop of an assassination by ninjas. Working together to defeat the Phantom they end up winning the competition. However, far from being happy, Kitajima insists they can do better at the next competition with more intensive rehearsals throughout the entire summer break.
Episode 10: With the summer festival approaching Haruhiko talks about the use of fireworks to mourn the passing of the dead. After he accidentally steps on her, Haruhiko's Phantom friend Ruru decides she is tired of being small. She meets a Witch Phantom who specializes in granting the wishes of other Phantoms. Ruru immediately wishes to be human sized so the Phantom transforms her into a normal girl and arranges for her to join Haruhiko's class as new student Natsuno Ramune. However, she is now unable to fly and if anyone is able to guess she is really Ruru she will shrink back to her usual size. Though instantly popular Natsuno finds it difficult to adjust to being human. Natsuno attends the summer festival with Haruhiko and the others but begins to feel guilty when everybody wishes Ruru was also there with them. Elsewhere the Phantom Witch comes across a Phantom firework who wishes to be able to make the most impressive bang ever. At the festival Natsuno is pleased to hear that even though she usually causes trouble for him, Haruhiko still wishes Ruru was there. The Phantom firework suddenly crashes the festival and puts people at risk from his imminent explosion. During the fight Haruhiko ends up attached to the firework. Needing to be able to fly again Natsuno reveals she is really Ruru to become small again and convinces the firework his explosion will be more impressive if he flies high into the sky with her, saving Haruhiko. Everybody is devastated at Ruru's death, until she reappears unharmed. Haruhiko ends up scolding her for worrying them but buys her the drink she wanted to apologize for stepping on her. Everybody watches the fireworks together.
Episode 11: Mai is seen protecting a young boy against a large Sand Phantom. Several days earlier everybody had been wondering what they were like as children. That night Haruhiko finds a box of items from when he was a child. The next morning Haruhiko wakes up a child version of himself with no memory of being a teenager. He heads to his old junior school where he believes he is in first grade. He is found by Kurumi who returns him to the club. It is decided that he should still attend his high school classes while Mai ends up volunteering to look after him at her house. Although polite and intelligent for his age Mai still struggles to attend school, work, fight Phantoms and care for Haruhiko and it takes a toll on her health. Haruhiko realizes Mai is struggling and does his best to be as little trouble as possible, so Mai takes him to the park. At the park Mai appears close to exhaustion and when an angry Sandbox Phantom, tired of being used by cats as a toilet, begins attacking Mai ends up collapsing. Unable to protect Mai, Haruhiko makes a wish to stop being a child and suddenly reverts to his grown up self again. He quickly summons the demon Cthulhu and easily defeats the Phantom, saving Mai who is shocked as Haruhiko is in only his underwear, having outgrown his clothes. Back at his home, Haruhiko, who does not remember becoming a child, wonders if it happened because he read a letter he wrote as a child describing a happy Sunday he spent with his parents. Mai knows the letter is a lie, Haruhiko's childhood fantasy, and wonders if Haruhiko's powers made him a child to experience that fun for real, in the same way Kurumi's powers transported her to her fantasy world to overcome her fear. Haruhiko is teased by the girls about how cute he was as a child.
Episode 12: Haruhiko starts with a brief explanation about how anything imagined from the human mind can turn into a Phantom. With summer break at hand, he and his party's efforts have paid off and they are now the team with the best results at the school. However, the students are later warned by Himeno about the appearance of a dangerous and powerful Phantom called Enigma, who attacks humans with special powers to steal them. Some time later, some students are attacked by Enigma, who steals their powers by kissing them. Haruhiko, Koito and Mai come to their rescue, apparently defeating and sealing Enigma, but it vanishes without a trace and the stolen powers do not return to their owners, implying that she is still on the run. Haruhiko keeps working on the device he found at the abandoned factory when he is called by his mother, whom he has not seen in a long time. After they reconcile she starts living with him again, much to his joy. One week later, the girls start worrying that Haruhiko has not had time to help them and upon watching him with his mother from afar, Koito feels a strange presence and they decide to pay a visit to his house in order to investigate. While having dinner, Mai is called by Himeno who informs her that Haruhiko's mother has been missing for a week. His mother attacks her, revealing that she is in fact being possessed by Enigma. Overpowered by Enigma's abilities, the girls watch helpless as she kisses Haruhiko and steals his powers, before leaving his mother's body and fleeing. While the girls worry about the unconscious Haruhiko, Ruru is also seen to have fallen unconscious at the same time Haruhiko did.
Episode 13: After the fight with Enigma Haruhiko has lost his ability to seal Phantoms. His mother remains unconscious in the Alayashiki hospital. Haruhiko meets his mothers new husband who gives Haruhiko a book from his childhood which she had cherished. Ruru has undergone a drastic personality change and is acting more like Haruhiko, i.e. polite, helpful and rather clumsy. It is suggested this is because Haruhiko no longer has powers and it has affected Ruru due to how close the two are. Elsewhere Koito is unable to track Enigma. Instead she goes to Haruhiko's house and demands he finish fixing the device from the warehouse as it can access the Alayashiki computers and possibly information on Enigma. Kurumi has Albrecht repair the device. They discover Alayashiki had been researching students abilities in order to artificially make Phantoms stronger for uses ranging from slave labor to disposable soldiers. One file focuses on Haruhiko and his relationship with Ruru. Enigma, the most powerful Phantom created, now hates humans. Enigma returns to Alayashiki Hospital searching for information. Haruhiko and the others are told by Himeno that Enigma wants data about Phantoms which she can combine with the Phantom summoning ability she stole from Haruhiko to summon and control all Phantoms and rule the world. Mai, Koito, and Reina fight Enigma who uses her stolen powers to easily defeat them. Haruhiko steps in and attempts to fight Enigma but is hurt while protecting Ruru. Himeno reveals that Ruru was created from Haruhiko's mind as an expression of the carefree part of his personality he had been repressing so she likely has the same powers Haruhiko does and Haruhiko can regain his powers by taking them from Ruru in the same way Enigma took them from him, with a kiss. After some hesitation Haruhiko and Ruru kiss, returning his summoning ability. It is revealed Enigma can only summon Phantoms Haruhiko had already defeated, whereas Haruhiko who has continued to improve, summons both the demons Cthulhu and Marchosias in their true, more powerful forms. They instantly defeat Enigma's summoned Phantoms and injure Enigma. Working together Haruhiko and his team manage to defeat Enigma who is happy humans are more complex than she first thought, and that she also enjoyed the time she spent with Haruhiko as his mother, before she disappears. Haruhiko happily sees Ruru has returned to her normal self. In the hospital Haruhiko's mother wakes up and they enjoy a tearful reunion. Alayashiki are investigated by the government. Every one of Enigma's victims regain their powers. Ruru is happy to learn she was once a part of Haruhiko and demands to be treated as his (older) twin sister in the future. Haruhiko realizes Ruru looks just like a character from the book his mother had kept. Life returns to normal and Haruhiko claims that even though the world tends to blur between fantasy and reality he rather likes it that way.
OVA: The story starts with Haruhiko explaining about human sense of vision, as well as optical illusions and visual preconceptions. The students of Hosea Academy goes for a summer trip by the sea. During the trip, Haruhiko states that he hates summer, and wishes that he is inside his house reading... until the other boys point out about the swimsuits the girls would be wearing. When they arrived, they are told that even though there are a lot of visitors each year, a sudden appearance of a Phantom scares people away, so they are asked to exterminate the said Phantom. In return, the lodging and food fees will be free. That being said, when asked about what the Phantom did, the lodge house owner refused to say anything. The first day pass by without anything happened, and they thought that since there is no visitors, probably the Phantom had moved to somewhere else. Unable to sleep, Haruhiko and Mai have a small talk under the moonlight, and Ruru disturbs them when the mood is just good. Before they know it, Koito, Kurumi and Reina join the gathering as well. During the next day, they play by the sea. Attracted by the girls in swimsuits, the Phantom appears and shoots water beam towards them, making a polka dot censor to make an optical illusion of them naked. Despite trying their best while being embarrassed, their attacks have no effect at all. Haruhiko summons Marchosias and Chtulu and is able to repel the censor effect for a moment, but being angry, the Phantom enlarges itself and shoots a huge amount of water to the air, this time creating white censor bar, with the same effect as the previous censor. Two of Haruhiko's male friends already give in to temptation of seeing the naked illusion, but Shousuke reminds them that it's more erotic if "you thought you can see it, but you can't" (though they are defeated in the end anyway). Figuring out the basis of the Phantom's ability of manipulating light and temperature, Haruhiko asks Koito to surrounds the Phantom with her fire voice to disperse the effect. With the illusion ended, Mai uses the sea to increase her water techniques, while Kurumi uses Albrecht to throw the Phantom in the air, which ends up eaten by Reina. With the case finally resolved, they feel that they can enjoy the rest of the vacation, until Haruhiko come back from the sea (he was swept away by the current when Mai and Albrecht attack the Phantom) without his swimming trunks, now really naked instead of just an illusion. As the four main heroines run away out of embarrassment, an equally embarrassed Haruhiko shouts that he hates summer (though Ruru likes it).