"Heaven's Lost Property" centers around Tomoki Sakurai, a teenage boy living in the peaceful town of Sorami. Tomoki’s life takes a dramatic turn when he encounters Ikaros, a mysterious winged girl who falls from the sky. Ikaros is revealed to be an Angeloid, a bio-mechanical being created by the inhabitants of the floating world Synapse. She bonds with Tomoki, recognizing him as her master, and her arrival sets off a series of events that disrupt his ordinary life.

As the story progresses, Tomoki learns more about the Angeloids and their purpose. Ikaros, despite her immense power and combat capabilities, exhibits a childlike innocence and a deep desire to understand human emotions. Her presence attracts the attention of other Angeloids, including the aggressive and competitive Nymph, who initially opposes Tomoki but later becomes an ally, and the mischievous yet loyal Astraea. Each Angeloid has unique abilities and personalities, often leading to comedic and chaotic situations as they integrate into Tomoki’s daily life.

The narrative explores the growing bond between Tomoki and the Angeloids, particularly Ikaros, as they navigate challenges posed by Synapse. The rulers of Synapse, led by the enigmatic Daedalus, seek to reclaim the Angeloids, viewing them as tools for their own purposes. Tomoki’s interactions with the Angeloids reveal deeper themes of free will, identity, and the nature of humanity, as the Angeloids struggle to define their existence beyond their programmed roles.

Throughout the series, Tomoki’s relationships with his childhood friend Sohara Mitsuki and his eccentric classmate Sugata are also explored. Sohara harbors feelings for Tomoki, which are complicated by the arrival of the Angeloids, while Sugata becomes involved in the mysteries surrounding Synapse and the Angeloids. The story balances comedic moments with emotional depth, particularly in its exploration of Ikaros’s growth and her evolving understanding of human emotions.

The series culminates in a confrontation with the forces of Synapse, as Tomoki and the Angeloids fight to protect their newfound bonds and assert their independence. The narrative weaves together elements of science fiction, fantasy, and romance, creating a story that is both entertaining and thought-provoking. The characters’ journeys, particularly Ikaros’s, highlight themes of love, sacrifice, and the search for meaning, making "Heaven’s Lost Property" a multifaceted exploration of relationships and identity.