Yuuki Yuuna Is a Hero

A month following their last encounter, the girls prepare to face off against the fifth Vertex, only for another hero named Karin Miyoshi to suddenly appear and defeat it single-handedly. The next day, Karin transfers into Yuna and Mimori's class, claiming herself to be a fully trained hero sent to supervise the newbies. She reluctantly joins the Hero Club, though is stubborn about becoming friends with the others. That weekend, as the girls plan to meet somewhere, Karin skips out on it, feeling she should not be led astray from her duty as a hero. Later that night, the girls show up at Karin's apartment, revealing they had planned to surprise her with a birthday party. At the end of the day, Karin is starting to get along with them.

Itsuki, who gets nervous when singing in front of others, is anxious about an upcoming test, so the Hero Club decide to go to karaoke to help boost her confidence. Meanwhile, Fu is unnerved by a message from Taisha telling her to expect the worst. As she continues to struggle with her nerves, Itsuki thinks about the burden placed on Fu, who has been looking after her ever since their parents died. Later, as Fu laments getting Itsuki involved with the Vertex, Itsuki assures her that she feels happy being able to fight alongside her. On the day of her test, Itsuki finds a letter from everyone encouraging her to do her best, allowing her to sing with confidence and giving her a goal of becoming a singer. Soon afterwards, as Fu contemplates with worst case scenario, another forestization appears.

Facing up against all seven of the remaining Vertex, the girls start to fight against the first one, only to be caught in a trap by another, who uses a loud bell to disable them. Itsuki manages to stop the bell, but then three Vertexes merge to form a single more powerful Vertex, proving resilient to their attacks. Not willing to give up, Fu and Mimori use their trump card, the Mankai form, to defeat the combined Vertex, while Itsuki uses her Mankai form to stop a smaller, faster Vertex from reaching Shinju. Fu then risks herself to buy time for the others to seal the remaining Vertex, whose core is discovered to be a massive one positioned in the stratosphere. Yuna and Mimori head to space together in order to fight against the core, using their Mankai forms to destroy it. Following the battle, Karin is relieved to find everyone alive and well and reports their victory to Taisha.

After receiving checkups at the hospital following their battle against the Vertex, Fu is revealed to have lost some vision in her left eye while Itsuki has lost her voice, both of which they assume to be temporary symptoms caused by battle fatigue. However, upon discovering Yuna has also lost her sense of taste and that she herself has gone deaf in her left ear, Mimori fears that these symptoms could be a side-effect of the Mankai form and gets in touch with Fu about it. Meanwhile, Karin, who hasn't been affected since she didn't use the Mankai form, has been avoiding going to the clubroom, as she fears she no longer has any purpose now that the Vertex are gone. However, Yuna manages to find her and convince her that, even with no-one to fight, the Hero Club will still carry on like it always has. Touched by Yuna's friendship, Karin convinces Taisha to let her stay at Sanshu Middle School until graduation, while the girls make plans for summer break.

Taisha rewards the girls with an all-expenses-paid trip to a hot spring inn during their summer break. The girls enjoy a day on the beach, have a delicious meal, relax in the hot springs, and tell some ghost stories. The next morning, Mimori reminisces about a ribbon she was holding onto when she lost her memory in an accident and wonders if their battles are really over. After the group returns home, making plans for the culture festival on the way back, Fu is summoned to the clubroom where she discovers everyone's old transformation cellphones, as well as a new fairy for herself, with Taisha warning her that another attack is to be expected.

After Fu informs the others that their battle isn't over yet, with each girl besides Karin receiving an additional fairy, the girls soon come up against another forestization. Discovering the remaining Vertex, finding it to be overflowing with cores, Yuna quickly disposes of them using the power of her new fairy, causing some worry amongst her friends. When the forest disappears, Yuna and Mimori end up separated from the others, having been summoned by a hospitalized girl, who reveals herself to be a former hero named Sonoko Nogi. Sonoko reveals to them the secret of the Hero System, in which heroes permanently lose the use of a bodily function in exchange for the power granted by the Mankai form, further revealing that heroes are effectively sacrifices to Shinju who can never die. On top of the shock both girls feel upon hearing this, Mimori is also saddened as she seems to know Sonoko, but is unable to remember her.

Yuna and Mimori relay what they've learned from Sonoko to Fu, who asks them not to tell Itsuki and Karin until they know for certain. Despite hearing from Itsuki's homeroom teacher how Itsuki has been suffering due to her missing voice, Fu remains in denial, hoping that things will eventually get better. The next day, however, Mimori reveals to Yuna and Fu that their fairies were actually created to prevent them from dying, even by suicide, proving that everything Sonoko said to them was true and that their symptoms are permanent. This leads Fu to become distressed, knowing that Itsuki's voice will never return and she will never achieve her dream of becoming a singer. Angered by having gotten everyone involved, Fu seeks to destroy the Taisha, even preparing to battle her way through Karin to this end. However, Yuna and Itsuki stop her from fighting, showing her they have no regrets joining the Hero Club.

Learning Mimori is at the center of the Vertex outbreak, Yuna and Karin chase after her into the barrier, learning what Mimori herself had learned. Before they can try to reason with Mimori, who believes destroying the Shinju is the only way to spare her friends from suffering, Yuna and Karin are forced to retreat from the Vertex.

Yuna is forced to fight against Mimori, who can't bear to lose her memories of everyone like she did with Sonoko, or be forgotten about herself. However, Yuna states her determined feelings to never forget about Mimori and manages to stop her. With the Vertex's final attack headed for Shinju, all of the girls, despite the afflictions caused by their Mankai forms, band together to block the attack, with Yuna delivering the final blow just in time, after which their fairies disappear, ending their role as heroes.