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.

Tragedy strikes the Sanctuary, and Elsa takes aim at both Roswaal's mansion and the village of Arlam. After being told that all these threats are cruel traps, Subaru can't help but give in to despair. While he's stuck questioning himself and unable to come up with a way out of the dilemma closing in on him, Otto shows up and punches him. Thanks to the many feelings packed in Otto's fist, Subaru finds his hope again.

Having been born with the "soul of language" divine protection that allows him to converse with non-human creatures, Otto Suwen's life has truly had its ups and downs. After being run out of his hometown because of his ability, he found his independence as a merchant, was attacked by the Witch's Cult, met Subaru... and now, his life is literally on the line in a deadly game of tag. To fulfill his part of the plan, Otto must evade Garfiel's vicious attacks in a desperate effort to buy time.

The missing Emilia was in the graveyard all along, her lost memories beginning to return due to Puck's disappearance. Confused and losing heart over the realization that she's forgotten such important memories, she tries her hardest to convey her feelings to Subaru. When the two of them leave the graveyard, they're awaited by Garfiel, who's been battered and beaten by Otto and Ram. He tries to prevent the Sanctuary's liberation by closing off the graveyard himself, but Subaru won't let him have his way without a fight.

As she attempts the first trial, Emilia finds herself in Elior Forest, where she lived when she was younger. Echidna snidely remarks on her audacity to set foot here after so thoroughly disgracing herself before, but Emilia responds with a bold smile and tells her she won't cave to the malice of a fellow witch. As they proceed deeper into the forest, they come upon a massive tree towering over its surroundings. At its base is a small, barred door, which Emilia identifies as the Princess Room where she was often sent to play as a child.

Despite a few inconveniences, like being unable to go outside when she wanted, young Emilia lived a happy life in a settlement of elves with Fortuna, whom she lovingly called "Mother." However, their peace was threatened by the arrival of the Sin Archbishop of the Witch's Cult representing Greed, Regulus Corneas. In the present, Shima appears before Subaru and the others as they wait outside the graveyard for Emilia to complete the trial, and she tells them of the events leading up to the birth of the Sanctuary.

Pandora, the Witch of Vanity, stands before Geuse and Fortuna. They both face her with all the strength they have. Meanwhile, young Emilia runs toward the place where the seal is, believing that everyone will be saved if she gives Pandora what she wants. But when she arrives, Pandora is already there, insisting that she hand over the key to opening the seal.

When Roswaal happily tells the story of how his romance with Echidna began 400 years ago, Beatrice rebukes him for casually calling it a "romance." Ryuzu interrupts to comment that Echidna saved her, as well. The one thing these three very different people share is their gratitude toward Echidna. But their days spent in both amicable and argumentative conversation about Echidna are brought to an end by one man's arrival.

Subaru tries to prevent the attack on the mansion by talking to Roswaal, but Roswaal refuses to let go of the wish he has clung to for 400 long years. Subaru takes Garfiel and Otto along as he hitches up the carriage to Patrasche and heads for the mansion as quickly as he can. Meanwhile, now that Emilia has completed the first trial, Ram asks her for a favor. Touched by the strength of Ram's feelings, Emilia reaches out to help her.

Frederica is gradually backed into a corner by Elsa's attacks. Then Garfiel rushes to the scene with a silver shield on each arm. The siblings' reunion after so many years is cut short when Elsa's knife violently clashes against Garfiel's shield. Meanwhile, Subaru heads to the forbidden library where Beatrice is. She's surprised when he enters the library and tells her that, after she spent 400 years there under a contract that might as well have been a curse, he's going to get her out.

After witnessing an unrealized present, Emilia completes the second trial and begins the third and final one. Ram and Puck are fighting their hardest to stop Roswaal. Each of them is doing it all for the sake of realizing their own goals. The battle between Garfiel and Elsa at Roswaal's mansion is also growing more and more intense. As Subaru is being chased by a guiltylowe, he declares that it's time to make use of his unparalleled knowledge of the modern world and lures it into a closet...

After completing the final trial, Emilia emerges from the graveyard into a blizzard heavy enough to block her vision. The people of the Sanctuary and the villagers of Arlam huddle together behind a giant wall of ice, created to shield them from the bitter cold by none other than the great spirit who was once contracted to Emilia. When Emilia touches the ice wall, something flows into her from within it. With a nod of acknowledgement to the voice she hears, she finally takes action.

The magic Roswaal is using to control the weather generates enough mana to attract the Great Rabbit, which draws closer to the Sanctuary in a massive horde. Emilia takes Roswaal and Ram to shelter in the graveyard with everyone else, but the Great Rabbit horde has already grown enough to engulf their surroundings. Just when all hope seems lost, Subaru and Beatrice appear before Emilia. So begins Subaru and Beatrice's first battle against the Great Rabbit, one of the Three Great Mabeasts.