After a sudden stop on his walk home from the convenience store, Subaru Natsuki finds himself transported to a fantasy world. Disoriented but surprisingly calm, he quickly realizes he has been dropped into a realm of magic, medieval-style culture, and demi-humans. His initial excitement is short-lived, as he is soon attacked by thugs. He is rescued by a beautiful silver-haired half-elf named Emilia, who is searching for a stolen insignia. Grateful, Subaru helps her, but that very night, both are brutally murdered.

Subaru then awakens back at the moment of his arrival in the city, alive and unharmed, though the people he met no longer remember him. After being killed several more times in different ways, he comes to understand his unique and horrifying ability: Return by Death. This power sends him back to a "checkpoint" in time upon his death, allowing him to redo events while retaining all memories of what happened. He discovers he cannot tell anyone about this power without the penalty of his heart being crushed.

Using knowledge gained from failed loops, Subaru successfully saves Emilia from the initial threat. She takes him to the estate of Roswaal L Mathers, a powerful margrave and her political sponsor in the Royal Selection to become the next ruler of the Kingdom of Lugnica. At the mansion, Subaru meets the twin maids Rem and Ram and the snarky, library-bound spirit Beatrice. As he settles into a new life as a butler, he discovers that threats plague the mansion. He is forced to die repeatedly, each time waking up on his first morning at the estate, to uncover the source of a demon beast curse and a shaman's attack. Through these loops, Subaru endures immense physical and psychological pain, witnessing the deaths of those he has come to care for. His persistence eventually saves everyone, earning him the deep trust of Rem, who falls in love with him, and a more wary respect from her sister Ram.

Subaru then insists on accompanying Emilia to the royal selection ceremony in the capital. His behavior there is disastrous; driven by pride and a misguided sense of heroism, he publicly humiliates himself and his allies. A frustrated Emilia cuts ties with him, unable to understand his actions, as she does not remember his previous sacrifices. Heartbroken and at his lowest, Subaru hears the mansion is under threat. Returning, he finds everyone dead and is killed. He enters a desperate cycle of failures, becoming broken and filled with self-loathing. At his breaking point, Rem gives him a powerful speech, refusing to let him run away and convincing him to "start from zero." Renewed, Subaru uses his wits, swallows his pride, and forges alliances, notably with the swordmaster Wilhelm van Astrea and the candidate Crusch Karsten. Together, they orchestrate a plan to defeat the White Whale, a legendary monster, and the sinister cultist Petelgeuse Romanee-Conti of the Witch's Cult, finally saving Emilia and the mansion's inhabitants.

The narrative deepens in the Sanctuary, a village trapped in a barrier by the Witch of Greed, Echidna. Subaru, Emilia, and Rem travel there, but Rem is erased from existence by a new Archbishop of the Witch's Cult, leaving everyone's memories of her intact except for her physical presence. Subaru is trapped in the Sanctuary with Emilia and the half-beast boy Garfiel, while back at the mansion, the assassin Elsa attacks. Subaru's Return by Death triggers countless times as he tries to save everyone in both locations. He enters Echidna's dream castle, where she offers him a contract for knowledge. He refuses after meeting other witches who warn him of her true intentions. Subaru learns that Roswaal, his own ally, has been orchestrating tragedy using a prophetic book to force Subaru to grow stronger, willing to sacrifice everyone to achieve his goal of reviving Echidna. Subaru breaks Roswaal's book, ending his foresight. He finally helps Garfiel confront his past, convinces Beatrice to form a contract with him, and supports Emilia as she overcomes her traumatic memories to free the Sanctuary. The season ends with the group unified, Subaru having accepted his own weaknesses, and Emilia determined to move forward as a candidate for the throne, with the vow to one day tell Subaru she loves him.