Amid dying countless times, Subaru finally led the troops to victory against the White Whale and struck down the schemes of the Sin Archbishop of Sloth. After overcoming a painful ending to his these ordeals, he was reunited at last with his beloved Emilia... only to learn that Rem's existence had been erased from the world, wiped out by the White Whale somewhere in the middle of his death loop. And now that the White Whale is defeated, Subaru and the others face a crisis no one could have expected.

After concluding their talks with Crusch, Subaru and Emilia return to the village of Arlam, intending to report to Roswaal and discuss what to do next. But they find Arlam deserted and learn that the villagers who had taken refuge in the Sanctuary with Ram have not yet returned. When Subaru and Emilia arrive back at Roswaal's mansion to find out where the Sanctuary is, they are greeted by Frederica, a young woman who used to work as one of Roswaal's maids.

On the way to the Sanctuary, Subaru unwittingly finds himself invited to a witch's tea party, where the hostess introduces herself as Echidna, the Witch of Greed. Subaru is alarmed, but Echidna encourages him to sit and drink his tea before it gets cold. When he somehow makes it back outside after a conversation with Echidna, he finds Otto lying on the ground, battered and beaten. Then, before he even has a moment to assess the situation, Subaru himself is attacked.

It's supposed to be his own room, a place he's supposed to be used to seeing, but Subaru can't shake the feeling that something is off. He's overcome by an indescribable sense of uneasiness, but being caught in his father Kenichi's armlock shakes it away. Subaru is stunned, but retaliates with a wrestling move of his own. As the two of them carry on, Subaru's mother, Nahoko, informs them that she's hungry and they should all eat breakfast together.

Having reached a place he can't return from, Subaru realizes just how much he has been given and how little he can do to repay any of it. After remembering what he must do, he says goodbye to Kenichi and Nahoko and heads to the school. Steeling his resolve, Subaru opens the door to the classroom, where he's greeted by Echidna in a school uniform. When Echidna says he arrived much sooner than she expected, Subaru responds that she looks good in the uniform.

After dying to Elsa's blade in Roswaal's mansion, Subaru awakens back in the graveyard, in the moment immediately after he passed the trial that required him to face his past. Just like the first time he returned there, he wakes Emilia and holds her to comfort her, then returns to Ryuzu and the others. He tells them that he passed the trial himself and suggests that he could complete the remaining stages of the trial in Emilia's place, but Garfiel is opposed.

Subaru had reached for the door, determined to save Rem from harm even if his current world would soon end. But instead of Rem, he found himself staring at Beatrice's library. Beatrice had remained silent throughout Elsa's attack and saved Subaru's life just moments before Elsa could claim it. Subaru shouts at Beatrice, demanding to know why she didn't help before everyone else was killed, and an intense argument ensues. Then Subaru catches sight of a familiar-looking book...

Subaru was caught and confined by Garfiel, but Otto shows up to rescue him. Garfiel can't leave the graveyard while Emilia is undergoing the trial, so Otto says this is their chance to get outside the barrier, but Subaru doesn't agree. However, after he learns that Ram will be helping them—that she has been ordered by Roswaal to help him, in fact—Subaru puts his escape on hold to have a talk with Roswaal.

After being eaten alive by a herd of unknown creatures resembling rabbits, Subaru awakens in a half-maddened state next to Emilia in the graveyard. As he pounds his head against the rocky ground over and over in anguish, he finds himself invited once again to a witch's tea party. There, he tells Echidna about his Return by Death ability, something he has never been able to tell anyone before. Echidna then begins to tell Subaru about the witch who gave him this power and set him on this agonizing path.

Subaru exits the graveyard to find the surroundings engulfed in deep black shadows. With the sudden appearance of the Witch of Envy, everything is swallowed up by darkness. After Garfiel rushes in to save him, Subaru tries to find a way to get them out of danger, but the Witch of Envy is relentless in her pursuit. Subaru finally offers himself as bait to stall her so Garfiel can intercept and attack, but he's helpless against the Witch of Envy, and everything continues to be engulfed by her shadows.

Subaru heads to Roswaal's mansion in hopes of finding out what's going on there and how he can fix it. He has Frederica and Petra evacuate to Arlam Village to protect them from Elsa's attack, then heads to Beatrice's forbidden library. He tries to get Beatrice out of the library, but her wishes don't align with his plans, and their discussion goes nowhere. Then, against all logic, Elsa finds her way into the forbidden library...

Subaru awakens in the graveyard with Emilia lying nearby. This time, he makes up his mind to save not only Emilia, but everyone in the Sanctuary and Roswaal's mansion from the threats that hang over them. Roswaal makes it clear that he will use Subaru's power to keep starting over by force if he has to, if it will allow him to achieve his own goal. What is driving Roswaal to go to such lengths? In search of the answer to this and many other questions, Subaru goes to see Echidna once again.

Subaru is shown several visions of events previously unknown to him during the second phase of the trial. When he feels as if he's worn away to nearly nothing, the one to stir him is the one who loves him more than anyone else... and is tougher on him than anyone else.