After having been forced to work on Kae’s behalf, Akari returns to Aoi Hikarizaka with her proverbial tail between her legs, only to find out that Aoi has taken up residence in an abandoned manor deep in the woods bordering the city. The manor seems to be the base of operations for a whole community of Puellae Magi, amongst which Akari recognizes several former members of Rui’s clique, including Miho Kawakami. As they return to school for the second semester, Hanako, Shinju and Koharu are surprised, not only to find Yasu has indeed transferred out, but also to find Rui’s victims have plastered the school hallways with flyers advertising a new school club focused on “soul therapy”. When they seek out the contact person mentioned on the flyers, a sophomore named Mirai Mizutani, their suspicions are confirmed, and Mirai excitedly invites the three to come and meet the clique’s new leader, who she claims is helping them to survive.

When Yuna reports back to the Bureau headquarters about the flyers, Shinobu urges her to focus on the manhunt for Cecilia instead. When Yuna asks Shinobu why she believes Cecilia to a threat to the city’s peace, it is revealed that Shinobu has been seeing visions of terrible calamity should Cecilia ever return to Mitakihara — visions so horrifying she is willing to curtail the city’s entire population’s freedom if it means avoiding them coming true. Meanwhile, Niko decides to make good on her promise of helping Koharu with her mother. When she tries, however, she is surprised to find out she can’t pull the amnesiac woman into the Dreamscape, probably indicating that her soul is already residing there. Hearing about this, Koharu theorizes that her mother’s missing memories may have been lost somewhere amidst the collective consciousness and urges Niko to find them as soon as she can. Niko tries, but instead finds René and Yui’s mother, who also appear to be missing some of their memories — implying that someone is meddling with the Dreamscape.

Following Mirai’s invitation, Hanako and Shinju finds out that Aoi Hikarizaka has more or less taken over as the new ringleader of Rui’s former clique. Though initially sceptical, Hanako becomes intrigued by Aoi’s noble ideations and begins frequenting the mansion to experiment with the effects of Aoi’s powers on her own. Nevertheless, the peaceful and welcoming atmosphere of the clique is disturbed when the hotheaded Miho Kawakami reminds the group that Chiemi Takahata is still in the Sixth Bureau’s custody. Seeing Chiemi as a hero for her murder of Rui Tomatsu, Miho warns that the Bureau might be out out to seize complete control over all Puella Magi activity in the city, and pleads Aoi to take preventive action, lest the clique’s members all become slaves again. Hearing about this call for action is enough for Koharu to decry the group as a bunch of zealots in way over their heads, but Hanako remains strangely compelled by it.

Thanks to Mei, who has also been invited to join Aoi’s clique, Yui learns about Aoi’s “soul therapy” as well and reports on it to the Sixth Bureau. Shinobu is far from excited to hear Aoi’s name, however, and reveals Aoi has been on the Bureau’s radar for a while — as a fugitive suspect in the murder of her uncle, the former Mitakihara police commissioner. As some of the Bureau’s troopers begin harassing the members of Aoi’s clique for the winged girl’s whereabouts, the girls are quick to close ranks. Much to their surprise, however, Aoi outright admits to the Bureau’s allegations, stating that her uncle beat her for years, and even profited off of his abuse by selling recordings to anyone willing to pay for it. Aoi explains she saw no other choice but to kill him when he started abusing other girls as well — convincing her friends that her deeds were justified. Nevertheless, the consternation quickly turns to worry, as some girls become convinced that the Bureau will be coming to arrest Aoi. When Miho escalates the conflict by alleging there is a traitor in the clique, Aoi and Hanako are forced to step in, though they cannot help but admit that Miho is onto something — everything seems to point at the Bureau preparing to bring an end to their peaceful lives.

The clique’s suspicions appear to be confirmed when, during the next weekly healing session, Aoi tearfully announces that one of the clique’s members has been attacked and hurt by a Bureau soldier patrolling the streets at night, though she refuses to disclose the victim’s identity out of respect for her privacy. Oddly enough, however, Shinobu appears to allege the exact opposite — that one of the Bureau’s soldiers was attacked by a Puella Magi the night before, and barely escaped with his life. In order to appease the ensuing calls for all-out war, Akari suggests asking the newspaper club girls for a more thorough investigation as to who is antagonizing whom. This idea ends up backfiring however, as it turns out Hanako, Koharu and Shinju aren’t on the same page when it comes to the Bureau, especially now the Sixth Bureau’s imposing on civil liberties and lack of transparency are starting to cause unrest among Mitakihara’s non-magical population as well.

That evening, however, all adult citizens of Mitakihara receive a video in their inbox from a prominent businessman named Masato Yasuda — Satomi’s father — who expresses his disgust at people defying the authorities trying to keep them safe. Accusing the current mayor of being incapable of guaranteeing the citizens’ safety and decrying his wishy-washy attitude vis-a-vis the Bureau’s presence in the city, Yasuda expresses his intention to run for mayor in the upcoming election, vowing to work together with the Sixth Bureau to keep the city safe. Predictably, this news does not go over well with Aoi’s clique, causing Miho to call for an operation to break Chiemi out of the Bureau’s custody, to which Hanako and Aoi eventually agree, ultimately joined by others, including Akari, Mirai and Miho’s best friend Kotori Ito. While the clique’s initial infiltration is a success, freeing Chiemi does not go according to plan, as the prisoner is furious to learn that by so blatantly drawing the Bureau’s attention, Aoi and her friends have put Akari back under the Bureau’s radar. Without hesitation, Chiemi uses her powers to disappear with Akari, leaving the other raid members behind to be arrested.

When Aoi, Hanako, Akari, Mirai, Miho and other clique members are brought before Shinobu, she is disappointed to discover they chose violence instead of collaboration. As she is about to unmask the assailants, however, Miho snatches a smoke grenade from one of the Bureau’s troops and drops it. In the ensuing panic, some of the Bureau’s troopers go against Shinobu’s orders and fire warning shots, though the clique eventually manages to escape. Upon the raid group’s return to the manor, however, Hanako realizes that Miho’s Soul Gem has been damaged by a piece of shrapnel. After Miho passes away, Kotori returns to the Bureau headquarters to wreak havoc, revealing her knowledge of Shinobu’s true identity as she hails from a clan that possesses a vast wealth of secret information about the world. Her attack is easily deflected by Shinobu, however, and she is teleported back to Aoi’s mansion by Mirai, who reveals her ability to copy her friends’ magic powers. In the meantime, Aoi shows Hanako the recovered Grief Seed of Walpurgisnacht, the Witch that nearly destroyed the city four years ago, which some members of the clique managed to unearth a couple of weeks earlier. She explains that through her ability to manipulate grief, she will be able to resurrect the gargantuan Witch under her own control, and use it as a deterrent against the Bureau.

Hanako is intrigued, but fails to understand how Aoi could pull off such impressive magic without corrupting her own Soul Gem, upon which Aoi unfolds her six wings, showing that five of them contain another Soul Gem. She explains that her magic allows her to use other Soul Gems as “batteries”, but Hanako is apprehensive as she realizes what this implies. Once again, Aoi wholeheartedly admits to having taken the Gems from others, but immediately adds that they either used to belong to truly wicked individuals, or were willingly handed over by fellow magical girls willing to abandon their physical bodies. Before Hanako has time to fully process what she’s just learned, she and Aoi are joined by a dejected Kotori. who does exactly that. Realizing she is more of a liability than an asset to Aoi in her current state, she begs Aoi to absorb her Soul Gem into her final wing, in the hope that it will allow her to cope with Miho’s death. Aoi reluctantly complies. Now with enough Soul Gems in her possession to enact her plan, she nevertheless senses Hanako’s unease with the plan, and attempts to sway her by revealing the identity of one of the Soul Gems she claimed — that of Hanako’s missing friend Ueno Asaharu. As Hanako recoils in shock, Aoi announces her intent to exhume Ueno’s body and bring her back to life as a reward for Hanako helping her to fulfil the raid’s true objective — retrieving Rui’s Soul Gem, which Aoi intends to replace Ueno’s in her first wing. This would make her powerful enough to finally summon Walpurgisnacht once more.