Episode 25

"Goodbye Once Again" is a bonus episode that is included in the 9th DVD/BluRay volume of Kill la Kill, which was released on September 3, 2014. On June 7, 2014, Shigeto Koyama and Hiromi Wakabayashi confirmed during a Q/A session at AnimeNEXT 2014 that the theme of the OVA will be "graduation".

Plot
Two weeks after Ragyō's defeat, Honnōji Academy has served its purpose and is to be decommissioned within a month. Ryūko is at its ruins with Mako and the Elite Four watching over a friendly match between Satsuki and Sanageyama. He strikes repeatedly, but Satsuki vanishes and breaks his sword. He then is questioned by the other Elites and says Satsuki's previous resolve is gone, and as such he couldn't bring himself to strike her. Below at the town, the citizens are packing up to leave, including the Mankanshoku Family. Mataro says goodbye to his gang, advising them to enroll in elementary once they move, and Sukuyo gives them "goodbye croquettes". His father reminds him they're moving as well, so he then goes to help packing by picking up their house and putting it into their truck.

At the remains of Honnōji Academy, the "First Graduation Ceremony" is about to begin. Ryūko, sitting by herself against a wall, intercepts Mako as she comes flying right at her in typical manner. She tells Ryūko that they will both be transferring to "Rinne High School" in Kanagawa. Mikisugi appears near the duo in his teacher garb, saying that he was invited to the ceremony as the History teacher. He then asks Ryūko how is she dealing with regular clothes since he was the one to arrange her and Senketsu to meet; reminding her that there are still Life Fibers in her. Mako jumps in and reminds them that Senketsu is alive within Ryūko, and she will always be wearing him. Aikurō expresses relief before revealing the futures of the Elite Four members: Gamagōri will be working at a relative's iron works, Nonon will inherit the Jakuzure Corporations, Hōka will pick an IT graduation, Iori will continue his study of Life Fibers as they move into college, and Uzu will work at home with his family while he continues kendo. He then says Satsuki is the only one left and Ryūko reply's that "she's trying to find a way to put down her sword. After spending her whole life sharpening its edge."

Atop of the ruined tower, Satsuki is enjoying a cup of Soroi's tea. Soroi tells Satsuki that the ceremony is about to begin in which she tells him to go make tea for all the students to drink and thanking him for all he have's done. As Soroi leaves, Satsuki was soon interrupted by a clone of herself and states that she knew they would come.

Ira Gamagōri demands the students' attention, declaring that the ceremony will begin with a speech from Satsuki. On cue, light shines from the tower above but instead in red and black glow heralds the appearance of the false Satsuki, declaring the graduation "nonsense". Uzu is question on what Satsuki was saying while Ryūko wonders if she was switching sides in which Nonon commented that she wouldn't do such a thing. Hōka points out to Iori about her outfit in which he states that she's wearing Junketsu. Satsuki is suddenly joined by doubles of the Elite Four, all wearing their first Goku Uniforms iteration. The false Elite Four echoes their master's words before going on the attack, transforming their uniforms into dark versions of the Elite Four's original Three-Star Regalia.

The students scatter within the sudden assault, with false Inumuta revealing that he has hacked his counterpart's computer to prevent him from analyzing the situation. Ryūko attempts to fight back, only to be met by the False Satsuki and her dark version of Junketsu Override. Luckily, Tsumugu arrives with weapons for everyone including a set of Tailor Dagger's for Ryūko, and customized DTRs for the Elite Four. Although the Elite Four balk at the idea of using the mecha, they realize that they have no other choice at the moment. As Tsumugu is quickly defeated by the false Ira Gamagōri, the Elite Four don their Nudist Beach uniforms and engage their doubles in the DTRs. Meanwhile, during Ryūko's battle against the false Satsuki, she demands to know where the real Satsuki is, only for false Satsuki to declare that she is the real Satsuki and that "a Kiryūin Satsuki with a broken spirit doesn't deserve to exist!"

The true Satsuki is showed to be trapped in the academy's engine room, strained to a machine with Life Fibers and trying to reason with her captor: Rei Hōōmaru. Rei demands to know why the heroes never bothered to kill her like they did Ragyō and Nui. Satsuki claims that her war with the Life Fibers taught her that everyone deserves a second chance, leading Rei to deduce that her quarry allowed herself to be captured. Satsuki says it's a way of putting away her sword and explains that she is willing to die if it satisfies Rei's grudge. The former REVOCS executive angrily retorts that one death will not compensate for the loss of her superior, stating the world has stepped in injustice, where the strong dominate the weak; believing that's the nature of humanity and its idiocy.

A flashback occurs to 20 years prior to the main series, revealing that Rei was originally an African child whose hometown was caught up in a civil war. Ragyō, who was searching for humans with high Life Fiber compatibility, saved the child by dismembering the soldiers. Learning that the girl had immense potential, Ragyō took her in, naming her "Rei Hōōmaru" and giving her a pair of green aviator sunglasses.

Back to the present, Rei states "this place" before giving a malicious chuckle. As the academy "eye" glows orange and the wall being lifted up, Iori and Soroi point's out that the Final Defense Apparatus Outside has been initiated and that it was meant to be used against the original Life Fiber but never put to use due to Ragyō takeover of the academy and is questioned on who started it. Rei states that she expected Satsuki to be an first rate source source for activating it but Satsuki replied that if she dies, it'll shut down in which Rei reveals Mako to be the backup source to it. Mako announce to Satsuki that she was lured in by a trail of cheese to distract her.

The Elite Four soon have abandoned their DTRs to fight their doubles directly, due to being unfamiliar with the controls of their mechs. Aikurō protests, even when Inumuta remotely controls the DTRs to distract False Sanageyama, declaring that they have lost their beauty. From the wreckage of his motorcycle, Tsumugu is appalled to learn that his friend actually liked the DTR's design. False Satsuki mocks Ryūko, telling her does she thinks that she could beat her without a Kamui, in Ryūko's response, states that she could beat a hollow phony like her to which the false Satsuki gives a devastating blow to Ryūko.

Rei pointed out in the speakers that the clones aren't fakes and that they're "literally the Elite Four's past-selves" to which Nonon points out it's Hōōmaru. Rei gleefully explains that she created her clones from the No-Star students' memories of their original reign of terror over the academy and that she used it to gives form with Life Fibers.

The Elite Four are increasingly pressed by their false doubles, who appear to match them in strength. Confident of victory, Rei prepares to strike, but Mako somehow hijacks the controls long enough to make the robot mirror her poses as she gives a speech to her friends, declaring that they're alot better than their past selves. Inspired by her words, the Elite Four suddenly turn the tables on their opponents: Nonon uses a sound-negation field to explosively reflect her double's attacks back to their source; Gamagōri punches into his clone chest and severs its Banshi; Inumuta sneaks behind his doppelganger and strikes its uniform's weak spot, a power button on the back of its head, before smashing it with a keyboard; and Sanageyama deflects his imitator's shinai barrage before slicing it in half. Finally, Ryūko locks blades with the false Satsuki and flips over her head, ripping out her Life Fibers in the process.

Angrier than ever at the loss of her creations, Rei unleashes the full power of the academy mecha, causing its arms to separate into multiple segments as it pulls itself free of the city. As Honnō City becomes greatly damage to the now-freed Honnōji Academy, chunks of land breaks up, leaving Ryūko to be clenching on the legs of the "Final Defense Apparatus". As she is struck by the falling debris, she falls into the a deep chasm below and as she continues to decline, resolves to keep fighting and protecting her friends. In space, a red flare is shown, as Senketsu voice echoes from above, telling Ryūko to "use this" as the Rending Scissors appears and enter Earth's atmosphere. The Scissors enter into the cavern, in which she grabbed onto it and use it to slow her descend and then proceed to run up the wall and then the mecha. As she dodges bullets, debris, and giant metal fist, declaring that she know what Senketsu was telling her and that she is "gonna take someone (Rei) who's stuck in the past and cut them loose from it!" She's then approached by the spirit of Senketsu, who agreed with what she'd said to which she understand what he meant and split the Rending Scissors in half.

The enraged Rei directs her mecha to pick up the S.S. Naked Sun to use as a weapon against Ryūko, but she responds by transforming her Scissor Blades into a gigantic scissor, dwarfing everything that stands, including the Honnōji Academy mecha. Ryūko calls out Rei, telling her to "stop dwelling on the past. Kiryūin Ragyō is gone! This is for you, for Honnōji Academy, for all of us - Our graduation from Ragyō! This is the ultimate graduation ceremony!" As Ryūko screams in adrenalin, she, along with the remains of the S.S. Naked Sun, destroys the Honnōji Academy "Final Defense Apparatus" and absorbs the Life Fiber within it.

Rei then returned to the captured Satsuki and Mako as they were trying to escape, lunging towards Satsuki, cutting her hair and the side of her neck. Satsuki told Rei that she "can't imagine the hell she had lived though because people don't understand, the world needs you". Rei replied, saying that she's not making any sense, to which Satsuki said "That's who we are." Rei drops her knife, accepting her offer. Ryūko appears, saying that Satsuki had finally put her sword away, which provoked a smile from both sisters. They all went to leave the now-sinking Honnō City.

As they walk out, the Elite Four are leading the students out of sinking city. Nonon tells Satsuki that they were waiting for her but was disgusted to see Rei alive. Satsuki tells them to take her as well, to which they all agreed. The Mankanshoku Family appears in their car, calling Mako and Ryūko to get in before the city sinks, so they enter the car and leave. As the evacuation upholds, Nonon questions Satsuki about Ryūko. Satsuki states that "I can see her whenever I want to." Satsuki uses the knife Rei dropped and cut her hair level, as "a small offering to our alma matter". Satsuki then orders all students to salute to pay respect to Honnōji Academy.

Aikurō comments about it being a nice graduation, to Tsumugu's agreement. As the Scissor Blades sink into Tokyo bay, Ryūko is shown sitting on top of the Mankanshoku's house, which is on the car that's driving on the road. Ryūko says that she really has outgrown sailor uniforms but Mako interrupts, saying that Senketsu will always be with her. As they both now sit on the house, the shining red star reappears, showing that Senketsu will be always in Ryūko's heart.

Characters

 * Ryūko Matoi
 * Satsuki Kiryūin
 * Mako Mankanshoku
 * Senketsu
 * Ragyō Kiryūin
 * Ira Gamagōri
 * Hōka Inumuta
 * Uzu Sanageyama
 * Nonon Jakuzure
 * Shirō Iori
 * Rei Hōōmaru
 * Aikurō Mikisugi
 * Tsumugu Kinagase
 * Mankanshoku Family

Trivia

 * The neon green color palettes used for most of the ghosts and weapons are based on the original concept color scheme for Senketsu.