Ground Control to Psychoelectric Girl

High school boy Makoto Niwa transfers to a new city, where he is introduced to his aunt, Meme Tōwa. Dreaming of living in a student home by himself, Makoto discovers the house is also inhabited by a girl wrapped up in a futon mattress, who is introduced as Meme's daughter and Makoto's cousin, Erio. After enrolling into his new school, Makoto tries to get to know Erio, who mostly speaks in confusing scientific jargon. While taking her to a supermarket, Makoto is able to undo the mattress, revealing Erio as a beautiful blue haired girl, who claims to be an investigator descended from aliens, and claiming that the Earth is being targeted.

Makoto spends the night eating convenience store dinners with Erio. The next day, Makoto rides home from school with his strange classmate, Ryūko Mifune. The following day, he gets acquainted with another classmate, Maekawa, who gets dizzy if she holds her arms above her head for more than 10 seconds. Later that night, Makoto goes with Erio to the beach, where she randomly walks into the sea, claiming she can fly. On their way back, they run into Maekawa, who reveals that Erio was a former student in their school who disappeared for half a year. Meme later reveals that Erio has no memories of the half a year she was gone and had started to believe in aliens. She also mentions Erio broke her leg while trying to fly on her bike, which caused her to start wrapping in her futon.

Makoto goes on a day out with Ryūko, who explains her stance on mysteries. Makoto relays what Meme had told him to Erio, though she seems reluctant to respond. Later, Meme tells Makoto not to get involved with Erio. Though he still wants to help her, Makoto decides to dispel her belief in aliens as the first step. He attempts this by taking her on her old bike and riding off a hill to disprove her ability to fly. The hill turns out to be a bit too steep, and they both go flying into the sea. Erio starts to come to terms with her being a simple Earthling and manages to introduce herself properly to Makoto.

Following his recent bike trip, Makoto is hospitalized with a broken arm. While in hospital, he is visited by Ryūko and Maekawa who are surprised to hear that he's living with Erio. After two weeks, Makoto is discharged from hospital and returns home, where he finally sees Erio again, who gives her thanks for bringing her back to reality.

As Meme reaches her 40th birthday, she decides to hold a sort-of-birthday the next day for Erio, who had missed her birthday during her disappearance. After Makoto gets Erio a present as per Maekawa's recommendation, Erio reveals she wants to get a job and try to return to society. Her reputation as a weirdo leads to her fail an interview, however, Meme manages to find her a job at the Tamura shop, run by her grandmother who believes in aliens.

Ryūko goes with her friend to the Tamura shop, where she encounters Erio and also spots Makoto. The next day, she decides to visit the place, running into Meme along the way. Afterward, Ryūko talks to Makoto about the bad reputation Erio has at school, mentioning it may cause him troubles if he is seen hanging out with her. Later, Makoto asks the old lady for some advice on the matter. A few days later, Ryūko and Maekawo visit the Tōwa household, where Makoto has trouble keeping Erio under control. As Meme returns and the suggests the girls stay for dinner, she openly hints that Ryūko might be a match for Makoto.