The film opens with Tomoki Sakurai, Soichiro Hoshi, and the New World Discovery Club in the middle of another unusual, if not typical, situation. A giant chicken wreaks havoc on Sorami City, and to counter it, a card from Saori Hayami as Ikaros helps Sohara Mina grow to giant size to fight the fowl. She defeats the chicken, but in a moment of clumsy bravado, she steps on Tomoki for staring up her skirt. The scene then shifts to Daedalus, Asuka Ohgame, who explains more about the Angeloids and their history, followed by a quiet moment where an Angel lies asleep in a pod.
On Earth, the film centers on Kazane Hiyori, Yoko Hikasa, the film’s main heroine, who introduces herself and recounts how she met and fell in love with Tomoki, weaving in memories from the two previous anime seasons as she quietly observes Tomoki and his friends, and grows closer to them.
After this recap, Hiyori asks to join the New World Discovery Club. Sugata Eishirou, Tatsuhisa Suzuki, is initially wary, remembering a Synapse-inspired Angel that resembles Hiyori and not fully trusting the club’s reality. Mikako Satsukitane, Ayahi Takagaki, argues that adding Hiyori will improve the club’s budget, and Sugata relents, which means Tomoki must participate more fully as well. Tomoki resists, so he subjects Hiyori to a series of playful, if lecherous, initiation tests to make her quit; she endures and completes them with embarrassment, yet her feelings for him remain unchanged. She is welcomed into the club and joins in many activities, and Tomoki starts spending more time with her. This shift leads Sohara, Nymph Iori Nomizu, and Astraea Kaori Fukuhara to believe Tomoki and Hiyori are dating, though Mikako hints that Tomoki might be using Hiyori to blackmail the others. When the trio confronts Tomoki, Hiyori overhears and steps in to clear the air, even confessing to Tomoki herself. Tomoki is left unsure of how to proceed, while Nymph and Ikaros realize that a relationship between Tomoki and Hiyori may be impossible.
In Synapse, Sugata asks Daedalus about the relationship between Hiyori and the Angel that resembles her. When Daedalus does not answer directly, Sugata recalls that he and Tomoki had once met in a way that briefly erased parts of their memory, and Daedalus confirms a connection to Synapse. Sugata resolves to investigate further, while Tomoki heads to meet Hiyori to deliver his response.
On the way, disaster strikes: Hiyori is run over by a truck and dies, her body vanishing and her existence erased from the memories of everyone not connected to Synapse. Sugata rushes to the Angels in pods, but the Hiyori he finds there is not recognized by him. The Master of the Synapse appears and taunts Sugata with the truth of forgotten memories, hinting that Hiyori is awakening. Tomoki, unaware of the full scope of these events, waits for Hiyori, while Nymph and Ikaros arrive and Nymph lies to him, saying that Hiyori will meet him tomorrow. A severe memory-wipe headache follows, and Nymph holds Tomoki, knowing that by tomorrow he will have forgotten Hiyori.
The next morning, Tomoki still remembers Hiyori, but everyone else has forgotten. He searches Sorami City in distress, while back in Synapse, Hiyori grieves that her time on Earth has ended; the Master of the Synapse offers her one last chance to see Tomoki. Tomoki confronts Ikaros and Nymph, who explain that they cannot reveal everything for fear of shattering Tomoki’s sense of reality. He collapses from the headaches, and Ikaros, Nymph, and Astraea stay by him as they follow a signal from Nymph’s radar and locate Hiyori. The reunion is cut short when Hiyori is transformed into an Angeloid and ordered by the Master of the Synapse to kill the trio. Hiyori uses time-manipulation to attack Sorami City and the Angeloids, and Nymph concludes that the only way to stop Hiyori is to kill her, though Ikaros objects. Tomoki stops Nymph, vowing to save Hiyori instead. The Master orders Hiyori to kill Tomoki, but Sugata arrives to help, and the three Angeloids stall her while they attempt to destroy the binding structure around Hiyori. They succeed in damaging the mechanism, but it does not fully free her. Nymph realizes that the dimensional mechanism that produces Hiyori’s time powers is reaching a breaking point, which could blow away Sorami City. Unable to stop the process, Ikaros traps Hiyori inside her Aegis to contain the blast, inadvertently trapping herself as well. Tomoki glides to the Aegis and is able to enter, bringing Hiyori back to her senses. Hiyori pleads for them to escape, but the blast will come soon, so she uses her hacking abilities to dispel the Aegis and kisses Tomoki before departing. She thanks him and remembers their first meeting as children, noting that it was because of him that she came to love Sorami City. Her time on Earth was brief but cherished, and she reaffirms her love for Tomoki before being destroyed. Tomoki breaks down in tears, vowing never to forget Hiyori.
Near the end of the credits, Sohara is shown viewing a scrapbook filled with pictures of the group having fun. A scene hints at Hiyori’s fading memory: a page appears where she had faded away, yet Hiyori slowly fades back in, suggesting she has somehow been revived.
In a post-credits moment, Tomoki stands at the overlook where he and Hiyori first met. A ray of light shines, feathers drift from the sky, he looks up, and a hopeful smile appears as the familiar sound of Hiyori’s bell ornaments returns, implying that she may have been revived.
