One day, while visiting her school's observatory in preparation for a meteor shower, a girl named Subaru comes across a mysterious greenhouse where she meets a frail boy. After leaving the room, finding it revert to the observatory before her eyes, Subaru encounters a small alien-like creature and follows it to a magically sealed classroom, where she comes across a group of girls in witch outfits, including her childhood friend Aoi. The girls and the creature, revealed to be a Pleiadian and the girls' president, notice potential in Subaru and give her a special broom, which brings her up through the clouds to a star-shaped gem that transforms her into a witch herself.

The next day, Subaru is surprised to find Aoi and the rest of the girls are all a part of her class, with her classmates seemingly having their memories rewritten. The Pleiadian believes this to be because of everyone's fates converging caused by his spaceship, which also seems to be related to Subaru and Aoi's contradictory pasts. With the story behind it put on hold, the girls teach Subaru how to ride her drive shaft, after which Subaru appears to be conflicted over her relationship with Aoi. She once again arrives at the mysterious greenhouse where the boy, Minato, assures her that Aoi is probably having the same worries as her. Taking his advice, Subaru and Aoi take to the skies to talk things over and become friends again.

As the girls feel downhearted over another loss against the cloaked stranger, not helped by the Pleiadian's harsh words, Subaru once again receives encouragement from Minato. Later, the cloaked figure attempts to steal another fragment from the girls, but a counterattack causes the fragment to wind up in the ocean, prompting the girls to dive in after it. However, some interference by the cloaked boy causes the fragment to launch up into the stratosphere. Managing to utilize Subaru's power, fellow member Itsuki helps bring everyone up to the stratosphere to obtain the fragment before the boy can.

The girls, learning that the next fragment is located in the Moon's orbit, are trained rigorously to prepare themselves to leave Earth. They also hear about a piano concert held by Hikaru's parents, who are trying to send piano music into space, much to the dismay of Hikaru herself, who barely gets to see them. Later, as the girls head for the Moon, they are once again interrupted by the cloaked boy, who ends up causing a blast. After having a dream, in which she laments to Subaru about not being able to listen to her father's song that she altered by herself, Hikaru awakes to hear the song being sent from Earth by her father, who believed a note she left that said she would be on the moon. After using the cloaked boy in order to catch the fragment, Hikaru manages to hear that her father kept the note she added to the song.

Aoi and Itsuki are chosen to play the prince and princess in a class play for the upcoming cultural festival. After encountering Minato again, Subaru hears from Itsuki about how, when she was younger, she got herself in an accident for which her brother got blamed, which led her to be conscious about causing people trouble with her own desires. Just then, as another fragment appears, the girls wind up on Saturn's rings, where they are once again confronted by the cloaked boy.

A mysterious band of light appears in the sky, which is revealed to be a faint remnant of the Pleiadian's spaceship that is slowly materializing. After recovering a fragment and returning it to the clubroom, Subaru discovers it to be a fragment that the cloaked boy had captured, using it to track the girls towards their base. Trapped inside the school by the boy's magic, which locks the others out, Subaru flees from the cloaked boy and comes across the greenhouse, where Minato reacts strangely to the earring that emerged from the fragment. Minato sends Subaru further into the garden to a door, which opens up the observatory doors, allowing the other girls to enter the school and pursue the caped boy, who brings the school into space in order to fight against them.

After Subaru plants the flowers that were left behind, she tells Aoi about Minato and the mysterious greenhouse, but she only becomes annoyed that she didn't tell her earlier. Later that day, Subaru seems to find Minato tending the garden, but he denies any existence of a greenhouse. Afterwards, the girls go to capture a fragment that has merged with a comet that is heading towards the Sun. While the others hold off the cloaked boy, Subaru and Aoi, realizing they both share the feeling of being left behind, make up with each other and manage to capture the fragment.

With the next fragment lying on the outer edge of the Solar System, Nanako, the Pleiadian's translator, volunteers to travel alone to its destination so the others can instantly warp there, having the Pleiadian act as her stand-in during her three month journey. As the months pass, Nanako laments her loneliness, having been separated from her little brother after he left with her mother to travel around the world. Arriving at the edge of the Solar System, Nanako comes across a lone planet, which she named Apate, and manages to call out to Subaru and the others, who join her in capturing the fragment, which causes Apate to gradually transform into a star. The girls soon arrive back to shortly after Nanako left, allowing her to celebrate her birthday and look forward to the events she would have otherwise missed.

With the school's cultural festival approaching, Subaru, who is making a planetarium with Minato for the astronomy club, offers to look after the fragments while the cosplay club hold their activities. While testing out the planetarium, Minato brings Subaru into outer space, taking her on a tour of the universe. During the trip, Subaru recalls how she once experienced something similar when she met a boy in hospital, which is revealed to be Minato.

Alerted to the fragments being stolen, Subaru discovers Minato is the caped boy as he uses the stolen fragments to draw the others towards him. While waiting in space, Minato thinks back to his childhood, where he met another mysterious boy named Elnath, helping him to search for crystals to repair his broken spaceship. Later, after Minato's first meeting with Subaru, Minato attempted to capture an engine fragment to grant Subaru's wish, only for Elnath's power to run out, revealing Minato had actually been in a coma the entire time. Refusing to accept this fate, Minato chose to pursue the fragments in order to change his destiny, casting Eldath aside and becoming consumed by darkness, while his other self slept until being found by Subaru in the magical greenhouse.

Upon waking up from her experience, Subaru finds she has lost her transformation powers and is no longer able to see the Pleiadian. Not wanting to remain depressed, the girls decide to turn their focuses to enjoying the cultural festival. After the festival, Aoi gives Subaru some encouragement before she and the others set off in search of the final fragment. Despite moving faster than the speed of light, the girls struggle to catch up to the fragment, but their determination to see things through points them towards their destination.

The girls discover the last fragment to be located within a black hole. With everyone needing to combine the fragments in order to drag the last one towards them, Subaru stops Minato from going into the black hole after it, assuring him that she'll be by his side and kissing him. With the spaceship appearing near them, Minato makes up with the Pleiadian, who is revealed to be Elnath, before helping the girls form six new black holes to draw out the remaining fragment. With his spaceship finally completed, Elnath travels to a new universe to carry on Minato's mission to save potential lives. Meanwhile, Minato takes the girls to the beginning of time, offering them the chance to live out different potentials, but they decide to be themselves. As the girls part ways with each other, Subaru decides to stay with Minato. Returning to the start of middle school, Subaru manages to reform her friendship with Aoi, as well as make friends with the other girls.