Kodaka Hasegawa, a recently transferred student who has trouble making friends due to his scary appearance, encounters his classmate, Yozora Mikazuki, talking to an imaginary friend. As they both talk about their troubles in making friends, Yozora gets the idea to create a Neighbors Club dedicated to help people make friends. After Kodoka and Yozora post up recruitment posters, another student, Sena Kashiwazaki, comes to join, saying that, despite her popularity, she also wants to make some true friends, though she does not get along well with Yozora.

Yozora decides that the first Neighbors Club activity is to play a co-op Monster RPG to improve their friendship. However, instead of playing co-operatively, Yozora and Sena constantly get in each other's way. The next day, Sena brings a girl game to the clubroom, which she ends up getting really into.

After Sena is caught playing an eroge and insists it's not perverted, Yozora has her read out the dialogue aloud to prove otherwise. Meanwhile, Kodaka's little sister, Kobato, feels jealous that Kodaka is spending more time with the Neighbors Club than with her. After encountering a swim-happy character in her game, Sena asks Kodaka to teach her how to swim. After the swimming lesson, Sena gets herself into trouble when she insults some guys hitting on her, forcing Kodaka to help her out. The incident reminds Kodaka of a friend he once had as a child, who taught him a lesson about friendship that Yozora strangely reacts to.

Kodaka meets 10-year-old teacher Maria Takayama, who was tricked by Yozora into becoming the Neighbors Club's advisor. Later, an effeminate-looking boy named Yukimura Kusunoki joins the club so he can study Kodoka and become more manly. Later, Kodoka saves a scientific girl named Rika Shiguma after she collapsed in the science room. Wanting to repay him in a somewhat sexual manner, Rika joins the Neighbors Club, where it is revealed she is also fascinated with curious dirty magazines.

Kodaka decides to start making healthy lunches for Maria, which makes Kobato jealous. Later, Rika has everyone try out a beta of a virtual reality RPG, which doesn't quite go as planned. After the game ends in utter defeat, Kodaka is surprised to see Kobato, who immediately clashes with Maria and decides to join the Neighbors Club so she can spend more time with Kodaka.

As Kodaka has a dream about his childhood friend, who he didn't get to say goodbye to before he moved, the Neighbors Club makes plans to go to a karaoke box. After feeling they are being cheated by the pricing system, Yozora and Sena end up in separate rooms while Kodaka and others share one. After the karaoke, Sena tells Kodaka that her father is interested in meeting him, which makes Yozora feel jealous.

As Summer rolls in, Kodaka asks Yukimura to provide Maria with her lunches in his place, though Yukimura misinterprets what qualifies as 'healthy food'. As the group decides to exchange e-mail addresses so they know who's coming into the clubroom over the summer, it is revealed Sena doesn't have a cell phone. She ends up getting the same model as Kodaka's, only to get spammed by a jealous Yozora.

With the air conditioner in Kodaka's house broken, Kobato takes inspiration from an episode of her favourite anime and starts wearing more normal clothes. More suited to the weather, she accompanies Kodaka to the clubroom where she clashes with Maria and finds herself adored by Sena. The club decides to go to the pool but find it crowded with popular people due a half-price offer, which proves to be too much for Yozora and Rika, who head home early.

As Yozora decides to have everyone dress in swimsuits for the day's club activities, Sena suggests that they go on a training camp to her private beach. The next day, Sena invites Kodaka and Kobato to her house to meet her father, Pegasus. After dinner, they are invited to stay the night, although Kodaka is forced to sleep next to Pegasus after he gets drunk.

The Neighbours Club reaches Sena's summer house and immediately hit the beach. They spend the weekend playing on the beach and listening to scary story attempts. After Yozora's story scares everyone, Kodaka gets called several times during the night to escort various girls to the bathroom, including Yozora herself.

The club decides to go to a matsuri festival for the purpose of getting takoyaki, which Kodaka is passionate about. While picking out a yukata, Kodaka explains to Sena about why he doesn't dye his hair. After having their fill of food, Yozora and Sena compete with each other at the stalls, before everyone gets together to set off some fireworks. After the last one is set off, Yozora's hair catches on fire, forcing Kodaka throw to a bucket of water on her to put it out. Soaked and humiliated, Yozora leaves and stays away from the club for the last week before school. When the new school term comes, Yozora arrives with her hair cut short, leading Kodaka to finally recognise her as his childhood friend.

Yozora recalls how she recognised Kodaka as her childhood friend, Taka, the moment he transferred in, but he wasn't able to recognise her, which led her to form the Neighbours Club. Yozora to Kodaka that she originally intended to reveal her true gender to him before she moved but was too embarrassed. She also acts to keep the fact they were childhood friends from the rest of the club and just call her by her regular name. Astounded by her new look, Rika gets Yozora to dress up in a boy's uniform as Kodaka contemplates what'll happen from now on.