"Boku ga Aishita Subete no Kimi e" is a science fiction romance anime that explores themes of love, identity, and the consequences of altering timelines. The narrative is divided into two interconnected storylines, each set in different timelines and featuring distinct protagonists whose lives are intertwined through a shared scientific experiment.

The first timeline is set in 2024 and centers on Koyomi Takasaki, a high school student who becomes romantically involved with Rika Mine, a classmate with a mysterious past. Their relationship deepens as Rika reveals her involvement in a secretive project called the "Time Leap Experiment," which allows individuals to send their consciousness back in time. The experiment is conducted by a shadowy organization aiming to manipulate events for their benefit. Koyomi becomes entangled in the project when Rika's life is threatened, leading to a series of events that force him to confront the ethical and emotional ramifications of altering time.

The second timeline takes place in 2049 and follows Nanoka Koyomi, a young woman who works as a researcher in a dystopian future where humanity is on the brink of extinction due to a catastrophic event known as the "Collapse." Nanoka is revealed to be the daughter of Koyomi Takasaki and Rika Mine, though she has no memory of her parents due to the timeline's alterations. Her story revolves around her efforts to uncover the truth about her parents' involvement in the Time Leap Experiment and her own connection to the project. As she delves deeper, Nanoka discovers that her existence is tied to the experiment's outcomes and that her actions could either save or doom humanity.

The two timelines converge as the consequences of the Time Leap Experiment ripple across both eras. The narrative examines how choices made in the past affect the future, and how love and sacrifice transcend time. Key themes include the fragility of human connections, the moral dilemmas of scientific advancement, and the enduring impact of personal decisions. The characters grapple with their identities and the weight of their actions, creating a layered and emotionally resonant story.