As Eruna Ichinomiya, a somewhat perverted schoolgirl, is pressured into choosing a high school, her cousin, Shigure Ninomiya, recommends his school, Mikagura Private Academy. Taking an interest in the principal's granddaughter, Seisa Mikagura, Eruna decides to take the entrance exam, which she passes by being able to see the school's feline teacher, who she names Bimii. At the start of her new school life, Eruna learns about the school's system, in which students are required to join one of the school's clubs, using points earned by battles against other clubs to improve their state of living. Stuck with the poorest living conditions due to not yet being in a club, Eruna attempts to join Himi Yasaka's Calligraphy Club, but is rejected due to her poor art skills. A few days later, however, Eruna is approached by Seisa herself, who invites her to join her Going-Home Club on a trial period on the condition that she act as the club's representative in a battle taking place the next week.

After learning about how students can use special abilities during club battles, in which student's must destroy all three of their opponent's crystals, Eruna pays a visit to each of the different clubs, learning about the various abilities the representatives have. However, Eruna struggles to come up with her own special ability by the time of her match, in which she must battle against Himi. As Eruna quickly finds herself on the defensive and goes into hiding, she comes across a sealed room and briefly sees a mysterious woman, who tells her that she has already possesses a power inside her. When she regains her senses, Eruna discovers she now possesses super speed and a finger laser ability called "Toy Gun", which she uses to destroy all of Himi's crystals in one go and win the match.

After learning about an upcoming rookie tournament for new students, Eruna reports her victory to Seisa, who claims that she only won because Himi held back and challenges her to a practise match with her club membership on the line. Prior to her match against Seisa, Eruna observes a practise match between the Astronomy Club's Asuhi Imizu and the Drama Club's Yūto Akama, with Yūto winning with a single strike. The match between Eruna and Seisa soon begins, with Eruna attempting to destroy Seisa's crystals whilst she is dozing off. However, Eruna's Toy Gun fails to activate and she is overwhelmed by Seisa's "Killing Art" ability, getting kicked out of the Going-Home Club as a result. Bimii, after informing Eruna that she needs to build more experience to use her ability properly, suggests that she form a club of her own, using the rookie tournament to attract potential members. Admiring her determination, Seisa lets Eruna bring her sleeping bag into her mansion.

With Eruna still struggling to use her Toy Gun properly, the Drama Club decide to put on an after-school beginner's class in the run up to the rookie tournament. As Eruna learns she will be facing against the Calligraphy Club's Meika Katai in her first rookie match, Yūto is feeling down as Asuhi reminds him of his younger brother, who was separated from him when their parents divorced, leaving him all alone. However, he is cheered up when Eruna and the other Drama Club members hold a party to mark the end of the beginner class. The next day, as Eruna faces off against Katai, her excitement from enjoying the duel allows to once again use her Toy Gun and win the match.

Eruna and Seisa take a look around the tournament's festival, where they end up standing in for Flower Arrangement Club's Sadamatsu Minatogawa, who is running a shooting gallery with his prized life-size Super Miracle Man doll up for grabs. After both Yūto and Eruna fail to even budge the doll, due to Sadamatsu protecting it with his ability, Seisa knocks down his second-best prize, which attracts more attention to the booth. Later, as Eruna hangs out with the Drama Club's Usamaru and Tonkyun, Seisa meets up with the Art Club's Kyōma Kuzuryū, who observes how she has changed since meeting Eruna. After Eruna clears the second round in the tournament, she witnesses Usamaru being overwhelmed by the school band's Azumi Sagara, who can manipulate gravity with her music, her victory prompting a harsh reaction from Seisa.

After holding a pep rally for Eruna, Shigure tells her about how he and Kyōma transferred to Mikagura from another school, which revolved around sports clubs, where Kyōma became distrustful of other people. As Eruna proceeds further in the rookie tournament, Tonkyun goes up against Azumi, managing to trick her into coming up close so that he can take advantage of her ability's weakness and win the match. This leads to Eruna and Tonkyun facing against each other in the fifth round, where Eruna announces her plans for a "Surrounding Eruna Ichinomiya with Cute Girls Club". As the two clash, Eruna brings out a new ability, Toy Bayonet, to win the match, igniting Kyōma's love of painting once more. After Eruna is inevitably eliminated in the quarter-finals, the tournament is won by a girl named Otone Fujishiro, who defeats Asuhi in the final round.

As Seisa reminisces about an old upperclassman, Eruna takes an interest in Otone, who appears to be just as weird as she is. Meanwhile, the Drama Club, noticing Asuhi feeling down about his defeat, decide to hold a party to cheer him up. After Eruna invites everyone to come along, Bimii, exhausted from escorting Eruna, mixes up an invitation he was supposed to give Asuhi with a message about a change in venue he was supposed to give Eruna. As such, Eruna misinterprates Asuhi's invitation as a letter of challenge and almost ends up initiating a match against Sadamatsu before Asuhi shows up. While waiting for the rain to stop so they can have a rooftop party, Asuhi explains how he came to love stars, after which Seisa uses her ability to put a stop to the rain and give Asuhi his starry-skied party.

The first-year students participate in an annual treasure hunt event, with Eruna paired up in a team with Otone, assisted by a Mecha Bimii. As Eruna clears the first set of checkpoints, Otone expresses her disinterest in teaming up with her and runs off. When Eruna injures herself after slipping off a cliff edge while searching for her, Otone takes her to her secret hideout to treat her injuries and have teatime with her. Things soon become hectic when Mecha Bimii transforms into a giant mech and goes on a rampage, but Eruna and Otone manage to use their combined abilities to make it out safely. Afterwards, as Otone agrees to help Eruna form her club-in-progress, Seisa grows concerned after witnessing Otone's Anticomplex ability.

Given until the upcoming midterm battles to find the third member for their club, Eruna and Otone use fake scandals in order to sneak promotion of their club into reports by the newspaper club, with not much result. As Eruna struggles to find members willing to join, Otone has the opposite problem of inadvertently scaring away anyone who is interested, as she is afraid they would get between her and Eruna. Upon stumbling across an empty classroom they could potentially use for their clubroom, Eruna is challenged by the newspaper club's Rumina Rikyū, who uses her Secret Memories ability to attack Eruna with embarrassing scoops from her childhood. Before Eruna is completed defeated, Otone uses her ability to plug Eruna's ears, allowing her to defeat Rumina. Thanks to Bimii transforming into human form to act as the club's third member, Eruna gets her "I'll Figure It Out Later Club" recognised and gains permission to use the clubroom.

Now having an official club, Eruna moves her sleeping bag out of Seisa's mansion and into her new clubroom alongside Otone. As everyone brings housewarming gifts, Rumina asks for Eruna's help in seeking out a rumored ghost haunting the school grounds. When Eruna and the Drama Club discover the ghost was most likely just Eruna hopping around in her sleeping bag, Bimii pretends to be the ghost to fool Rumina, but soon gets caught in a mysterious void. Meanwhile, Otone confronts Seisa over why she won't go see Eruna, deciding to fight against her when she refuses to listen. As Otone pushes her further into a corner, Seisa finds herself unable to use her Killing Art, only being saved when Eruna arrives on the scene.

After Otone runs off, Eruna becomes shocked when she notices some strange scars on Seisa's back. The next day, Otome apologises to Eruna, who asks her to help her train for the upcoming midterm battles. As Seisa stays away from the battles and shuts herself in, her Killing Art ability starts going out of control, causing temporary cracks to appear around the school. Investigating the school's photography club, Eruna stumbles into a different dimension and comes across Bimii. He explains that during her first year, Seisa was betrayed by the photography club upperclassman she admired, who seriously injured her with her ability, prompting Seisa to use her Killing Art to seal the clubroom away and shut herself in. With Seisa's Killing Art growing more unstable by the minute, the school itself starts becoming warped, with Eruna and Bimii falling through a sudden crack.

Eruna briefly sees a vision of people resembling Seisa, Shigure, and the girl she met when she first got her powers, before winding back in the real world, where the school has turned into ruins. Shigure explains that the people she saw were their ancestors who founded Mikagura Academy, stating that Eruna's ancestor gave Eruna her powers so that she could help Seisa. Eruna rushes over to see Seisa, asking her to join her club if she manages to win the midterm battles. After giving her thanks to her ancestor, Eruna makes it to the finals, where she is supposed to fight against Kyōma, but the others arrange for Seisa to fight against her instead. With Seisa regaining control of her power from the enjoyment of the battle, both combatants bring out their full power against each other. After the match ends in a draw, Seisa decides to join Eruna's club, which she names the "Afterschool Paradise Club".