In the new universe Madoka created, Wraiths prey on emotions and Mami, Kyoko, and Sayaka work together to fight them in Mitakihara. Sayaka locates a Wraith colony and engages it alone, notifying Mami but not Kyoko of its location. Afterward, Sayaka and Kyoko argue about their mistakes, eventually brawling away from Mami until they exhaust themselves. They reconcile awkwardly and share pocky.
The next day, Hitomi presumably confesses her feelings for Kyosuke to Sayaka and gives her an ultimatum to confess. Later, Sayaka is distracted by these feelings and struggles in battle. She walks home, preoccupied with thoughts of Kyosuke and Hitomi. Kyoko confronts her, suggesting a dark solution to eliminate Hitomi's feelings for Kyosuke with a Wraith. Sayaka rejects the idea and accuses Kyoko of selfishness. Their argument escalates into a rooftop battle, with Kyoko eventually gaining the upper hand. However, Sayaka uses her cape to set up a trap and declares victory. Despite their differences, Sayaka agrees to continue working with Kyoko for Mami's sake but warns her to stay out of her personal life.
Sayaka recalls Hitomi's confession about liking Kyosuke and giving Sayaka one day to confess her own feelings. That night, Sayaka debates telling Kyosuke but is interrupted by Kyubey, who warns her of a strong Wraith nearby. Following Kyubey, Sayaka finds the Wraith targeting a busy shopping street, where Hitomi is among the crowd. Sayaka fights and defeats the Wraith, saving Hitomi unnoticed. From a rooftop, she sees Kyosuke approach Hitomi, and they walk away together.
Later, at the station, Kyoko and Mami discuss Sayaka and Mami urges Kyoko to apologize for her past behavior and bring Sayaka back. Meanwhile, Sayaka fights a growing horde of Wraiths alone, but eventually succumbs and allows them to absorb her emotions. Kyoko intervenes and saves Sayaka from the Wraiths, but Kyubey stops them by warning that Mami is in danger. Mami battles a giant Wraith whose power overwhelms her and Sayaka and Kyoko arrive to help. Mami devises a plan to defeat the Wraith and trusts Sayaka with the riskiest part. As the plan unfolds, the Wraith traps Sayaka and starts consuming her memories and emotions. Kyoko pleads for Sayaka to fight back and Sayaka regains her resolve, transforms, and defeats the Wraith.
In a vision from Madoka, Kyosuke plays in an empty auditorium as Sayaka watches. Madoka takes her hand and takes her to the Law of Cycles.
At the station, Mami and Kyoko realize Sayaka has been taken by the Law of Cycles after fighting a Wraith. Homura, now present, holds Madoka’s ribbons and softly says her name, leaving the others confused.
Saotome introduces Homura as the new transfer student. She later fakes feeling unwell and leaves the classroom. On the rooftop, Homura meets Mami and Kyoko where Mami explains they’re meeting to discuss a giant Wraith.
Homura sits atop a building, contemplating her Soul Gem and its time shield, now useless in the new world. Unable to find a reason to keep it, she discards the shield, which creates a portal upon hitting the ground. Entering the black hole, Homura finds herself in a surreal world that feels eerily familiar. Hearing Madoka’s voice, she runs toward it, but the ground gives way to strands of hair, and she faces Kriemhild Gretchen. She runs away and realizes her shield contains a Witch, despite Witches no longer existing in this world.
Homura considers destroying the shield but hesitates, fearing that Madoka, who fights Witches eternally, might be inside. Instead, she erases her memory of the shield with magic and vows to protect Madoka’s world.
At night, she tells Kyubey of the Law of Cycles and Madoka, but Kyubey doubts Homura. Homura descends a building with Kyubey on her shoulder and defeats them. She fights Wraiths with Mami and Kyoko and later, Homura faces the giant Wraith alone, but the Wraiths trap her. Mami and Kyoko fight their way to Homura, who awakens to find herself de-transformed and surrounded. A Wraith takes Madoka’s ribbon and Mami and Kyoko find Homura unconscious on the street.
Homura dreams of a barren desert, hearing Madoka’s voice calling her name and wakes in Mami’s bed. When Mami asks her to transform and summon her weapon, Homura struggles to do so. Mami deduces the Wraiths stole some of her magic and points out her Soul Gem’s unusual state. Homura recalls the Wraiths also took Madoka’s ribbon and asks if defeating the wraith could restore her magic. Mami doubts it but insists they work together. Homura confuses Mami by altering her memories, thanks her, and leaves.
Homura encounters Kyoko, who offers to exchange information on the giant Wraith, agreeing only if she gets to finish it off. Mami returns to her apartment and senses a Wraith’s presence. She cautiously enters her home, confronting mutant Wraiths who've taken the form of her parents. Meanwhile, a Wraith whose taken the form of Madoka wanders the streets with a ribbon around her neck.
Homura confides in Kyubey that her powers haven’t recovered, even with grief cubes. Kyubey theorizes the Wraiths targeted her magic specifically and notes their disappearance after her defeat. Mami passes them without a word. Later, Mami cryptically asks Kyoko how she’d react if the dead reappeared, then decides they should patrol separately.
Kyoko meets Hitomi, who overheard her conversation with Mami. Hitomi seeks answers about Sayaka’s disappearance and blames herself. They both feel guilty, but are distracted as Sayaka appears on a light post and calls to them. She jumps down, laughing as she explains how she ended up in another dimension, unaware a month had passed. Kyoko is stunned, but Hitomi tearfully apologizes for breaking her promise about Kyosuke. Sayaka questions if Hitomi’s guilt stems from thinking she ruined Sayaka’s chance to confess and demands Hitomi “hand over” Kyosuke as proof of her sincerity. When Kyoko protests, Sayaka accuses her of betrayal too, blaming her for not sharing grief cubes. Kyoko recognizes that it is not Sayaka and Sayaka’s Wraith powers flare as she attacks Kyoko.
Elsewhere, Mami walks through a park, speaking to the indistinct forms of her parents. She reminisces about her struggles growing up alone but feels grateful for being able to see them again. She transforms and destroys the Wraiths masquerading as her parents.
At the station, Wraith Sayaka reveals its true form and flees. Kyoko follows her after telling Hitomi to forget everything and that Sayaka is dead. Chasing the mutant Wraith, Kyoko is swarmed by smaller Wraiths. Meanwhile, Homura encounter Kyoko, but Mami intervenes, revealing this Kyoko is a Wraith too. When Wraith Kyoko shows time manipulation powers, Homura hears a mysterious voice offering help. Following its guidance, she and Mami trap the Wraith and destroy it with a Tiro Finale.
As the smoke clears, the real Kyoko arrives, confused. Mami confirms her identity, and Kyoko explains the Wraith she saw had turned into Sayaka. Mami suggests they rest and meet tomorrow, warning them to stay vigilant at night. Later, Homura hears the voice again. She turns to see Madoka, dressed in white and smiling, telling her she missed her. 'Madoka' reveals she's a Wraith. She says Homura's power disrupted the Wraiths, creating mutations, and asks Homura to defeat the giant Wraith responsible. Homura is skeptical, but allows Wraith Madoka to stay at her apartment temporarily.
At Homura's apartment, Kyubey confirms Wraith Madoka carries Homura's magic and detects curses mixed within her, likely causing the mutations. Homura asks Kyubey to keep the Wraith's presence a secret. Meanwhile, Homura, Mami, and Kyoko strategize to avoid Wraith tricks while searching for the giant Wraith.
One night, Wraith Madoka confronts Homura and tells her that Homura's heart is broken, leaving her unable to trust or feel. Homura vehemently denies this, declaring her unwavering love for Madoka and determination to fight for her memory. Wraith Madoka claims to embody Homura’s heart, but Homura rejects her and calls her an enemy.
When they meet, Mami expresses concern for Homura, urging her not to shoulder everything alone. Homura lashes out, accusing Mami of seeing her as a nuisance. Mami apologizes and reminds her they are friends. Homura apologizes and leaves. She later questions Kyubey about her wish as a Magical Girl, which he doesn't know about. Homura realizes her memories of Madoka might be fabricated by her own memory magic and doubts everything she's fought for. She runs through the rain and Wraith Madoka appears in front of her. Homura ignores her and runs into Mami and Kyoko, who confront her, sensing something is wrong. Wraith Madoka clings to Homura, and Homura reveals that Madoka sacrificed herself to become a goddess who saves Magical Girls. Kyoko takes offense, accusing Homura of dishonoring Sayaka’s memory. Homura admits she rewrote her own memories and no longer knows what is real. She breaks down, unable to believe in anything, and begs Madoka for salvation. Mami tries to save Homura by attacking the Wraith, but Wraith Madoka defends herself and transforms. She kisses Homura’s Soul Gem and unleashes her power, floating in the air with Homura and teleporting away.
Homura sits in her apartment with Wraith Madoka as Kyubey emerges. He notes that Homura’s emotional energy is gone, leaving her Soul Gem stagnant beyond the reach of the law of cycles. Wraith Madoka senses a giant Wraith as hundreds of smaller ones head toward the clock tower.
At a park, Mami and Kyoko discuss Homura's absence and her bond with the Wraith. Suddenly, miasma fills the park and Wraiths surround them. The girls transform but hold off attacking, realizing the Wraiths are ignoring them and decide to follow. In the city, they find dead bodies, confusing Kyoko since Wraiths don’t kill. Wraith Sayaka appears, and Kyoko fights her, telling Mami to follow the smaller Wraiths. Kyoko frees herself, destroying the Wraiths with a powerful spear attack, though her Soul Gem darkens.
Meanwhile, Mami fights Wraith Mami and Wraith Kyoko. As she prepares a fights, Wraith Madoka takes Homura’s ribbon and shoots magical arrows on the Wraiths. emitting a radiant aura. She shoots an arrow into the sky, raining magical arrows on the Wraiths. When the dust settles, Mami sees Wraith Madoka standing before her. The mutant Wraiths attack, but Wraith Madoka protects Mami. She hesitantly accepts Wraith Madoka’s outstretched hand, and time stops around them. Together, they defeat the mutants using Mami's Tiro Finale.
At the clock tower, tendrils transform into a massive Wraith-like creature. Wraith Madoka reveals to Mami and Kyoko that the creature has transcended Wraithhood and now threatens all life. While she urges them to flee, Mami decides to fight. Kyoko, tasked with evacuating civilians, gives Mami grief cubes to cleanse her Soul Gem. Moments later, Kyoko is caught by the creature’s tendrils. Wraith Madoka rescues her, but Kyoko's Soul Gem is already drained. Kyubey confirms anyone touched by the creature dies immediately and urges Mami to escape.
Wraith Madoka battles the creature’s Familiars, but they overwhelm her. As she falls, Homura, who has been watching, suddenly remembers everything. She realizes the transformed Wraith is a Witch and proof of Madoka’s existence. Determined, she rushes to save Wraith Madoka and catches her mid-fall, embracing her. Homura now understands the power behind it all stems from her shield.
Homura recalls the Witch in her shield while pinned under debris. She sees Wraith Madoka injured nearby, holding her ribbon. Homura reaches out, and Madoka takes her hand, reassuring her. Inside herself, Homura meets a version of herself in a white dress. This Homura is her magical power personified, who explains that Homura’s new memory powers were born from her and Madoka’s deep connection. This power separate from current universal laws interfered with the shield’s time magic, linking it to Madoka. The shield’s curses caused the Wraiths to mutate and threaten the world, transforming into a true Witch with the potential to destroy everything. Determined to stop the Wraiths, Homura asks her magic for aid. Sayaka, Mami, and Kyoko, in Wraith forms, challenge Homura’s resolve, warning her of the pain of losing the shield and doubting Madoka again. She refuses to abandon the world Madoka saved and resolves to fight for it instead. She declares her feelings for Madoka and asks her magic to transform—not as a shield to protect Madoka, but as a weapon to destroy her enemies. The white-dressed Homura then becomes her Soul Gem.
Homura transforms into a Magical Girl, wielding her black bow and magic wings of corrosion. She destroys the Wraiths' Familiars with a powerful arc of magic and fires an arrow at the giant Wraith, cracking it open. As she pushes the arrow deeper and finds her old time shield. Just before she reaches the shield, Familiars restrain her. Ultimate Madoka appears and pushes her hand to help her reach it. Homura shatters the shield, unleashing a blinding light that destroys the giant Wraith.
Homura awakens in an unknown realm, where White-dressed Homura explains time is rewinding due to Madoka’s intervention. She warns Homura that their memories will be erased but promises to support her if her resolve wavers. White-dressed Homura is shown inside Homura’s Soul Gem.
