Ryuko Matoi transfers into Honnouji Academy, a high school dominated by its fearsome student council, who wear powerful Goku Uniforms that grant them superhuman abilities. Searching for clues to her father's murder, Ryuko confronts the student council president, Satsuki Kiryuin, saying she is looking for the owner of the other half of a giant scissor blade she wields.

Weakened by her battle, Ryuko flees Honnouji Academy before collapsing in the street. Rescued, she's given food and shelter for night, and upon returning to the Academy faces off against Omiko Hakodate, the Girls' Tennis Club Captain, to repay the favor.

Having kept her end of the bargain, Ryuko demands answers from her homeroom teacher, Aikuro Mikisugi, and learns the secret behind the power of Senketsu and the Goku Uniforms. Meanwhile, Satsuki Kiryuin returns home to claim a power of her own.

While Senketsu is laundered, Ryuko is faced with "No-Late Day", a school event where students must navigate a trap-filled obstacle course and reach school on time, or else they will be expelled. She and Mako make their way across the perilous course, along with an injured girl named Maiko Ogure, while Mako's family attempt to deliver Senketsu to Ryuko. After hijacking an armored bus, the girls manage to make it to the school grounds with 15 minutes left. However, Maiko is revealed to be a member of the disciplinary committee, who steals Senketsu and puts it on herself in a bid to overthrow Satsuki. However, she is immobilized by the freshly washed Senketsu's starchiness, allowing Ryuko to retrieve him. With five minutes remaining, Maiko sets off one more trap to send Ryuko and Mako back to the start of the course. They two fortunately reach class on time using an express cable car, while Maiko is expelled for her treachery.

A mysterious sniper named Tsumugu Kinagase attempts to assassinate Ryuko, but is interrupted by the gardening club, who he manages to defeat. After dealing with the biology club, Ryuko is attacked by Tsumugu, who pins her down and attempts to force her to strip, but is forced to retreat when he is interrupted by Aikuro. As Aikuro and Tsumugu talk later that night, Tsumugu explains that the Kamui could prove a great threat if left alone. The next day, Ryuko confronts Tsumugu, who attacks her with needles that drain power from Goku Uniforms and Kamui, whilst they both come under attack by the gardening, rakugo and hyakunin-isshu clubs. With the clubs wiped out and Ryuko backed into a corner, Senketsu gives himself up to protect Ryuko, but Mako stands up to Tsumugu and returns Senketsu to Ryuko. As Tsumugu comes to understand the bond between Ryuko and Senketsu, they are confronted by one of the four elites, Nonon Jakuzure, but manage to escape.

After learning of his connection with Tsumugu, Ryuko tries to press Aikuro for more information, but does not get much outside of his organization's name, Nudist Beach. Meanwhile, another of the Elite Four, Uzu Sanageyama, gets permission from Satsuki to fight against Ryuko himself. The next day, Uzu challenges Ryuko, facing against her in his Three-Star Goku Uniform, Blade Regalia. He has the advantage due to his fast eyesight reading all of Ryuko's moves, but Ryuko overcomes this by using a part of her uniform to block Uzu's vision, allowing her to defeat him and destroy his uniform. Not wanting to give up, Uzu undergoes a drastic operation to sew his eyes shut, and challenges Ryuko again, this time using his other senses to predict her moves and completely overwhelm her. However, before Uzu can deliver the final blow, his Goku Uniform overheats due to him being more powerful than it can handle, giving Ryuko the opportunity to escape.

Hearing about how many students have been starting their own clubs in order to become eligible to get better uniforms, and thus better living rights, Ryuko decides to start her own Fight Club, assigning Mako as the club president to handle all the paperwork and meetings. As Ryuko increases the club's reputation by defeating other club presidents, Mako manages to earn a One-Star Goku Uniform, upgrading the Mankanshoku family to a better apartment. Mako's determination to preserve her family's newfound happiness moves the family up to an even more luxurious lifestyle. However, as Mako becomes more serious about her duties as club president and the other family members indulge in their wealth, Ryuko starts to feel lonely as the family finds less time to spend together. Just as Ryuko decides to resign from the Fight Club, Satsuki gives Mako a Two-Star Goku Uniform, telling her to defeat Ryuko if she wants to keep her life of luxury. Ryuko decides to take the brunt of Mako's attacks, which leads to Mako eventually realizing the error of her ways, deciding to disband the Fight Club and return to her life in the slums. Meanwhile, Satuski reveals that by using Ryuko to purge the weaker clubs, she will restructure the student council by holding a reprisal general election.

Satsuki announces her new election system in which students must survive a seven-day battle against each other in order to stand out on top and earn Goku Uniforms, sending the entire school into a state of emergency. Meanwhile, Ryuko takes Mako to the ruins of her old house, where she tells her about the circumstances surrounding her father's death. Finding no further clues in the basement where she found Senketsu, Ryuko and Mako head home, only for their scooter to run out of gas. They end up encountering the disciplinary committee chair and one of the Elite Four, Ira Gamagoori, who, having just attained his driving license and is taking the week off, offers to take them to a gas station. During their drive, they are attacked by the automotive and airsoft clubs, who are targeting Ira's Three-Star Goku Uniform, Shackle Regalia. Recalling how he first met Satsuki, Ira unleashes his uniform, which uses the power of masochism to evolve into Scourge Regalia and lay waste to his opponents. After a week passes, Honnouji's strongest assemble for the Sudden Death Runoff Election, with only Ryuko and the Elite Four making their way to the top. There, Satsuki challenges Ryuko to defeat each of the Elite Four in exchange for details concerning her father's death, her first opponent being Ira.

As Ryuko awaits the time for her battle against Ira, Aikuro asks her to drop out of the match, warning that she is not ready to face the Elite Four, to which she naturally declines. The battle soon begins, with Ira activating his Shackle Regalia, attacking himself in order to provide the power needed to transform into Scourge Regalia. Ryuko soon learns that the Shackle Regalia also serves as an armor protecting its life fibers. This pushes Ryuko into a corner, as she is unable to damage the Shackle Regalia without powering up the Scourge Regalia form. Undeterred, Ryuko keeps on attacking, forcing Ira to bring out Scourge Regalia's full power, attempting to forcefully mold Ryuko into a model student. However, Senketsu sets a plan into motion by pulling Ryuko out of her synchronized mode, allow her to use Senketsu's fangs to break into Ira's uniform and destroy it from the inside using a new form, Senketsu Senjin (鮮血閃刃?, Senketsu Blade Flash), winning the match. With Ira defeated, Ryuko prepares to face up against her next opponent, Houka Inumuta.

Houka uses his Three-Star Goku Uniform, Probe Regalia, to analyze Ryuko's fighting abilities and anticipate her movements. When Ryuko counteracts this by fighting haphazardly, Houka resorts to cloaking himself and fighting her while invisible. Ryuko counters again by expanding and draping Senketsu's eye across the battle arena, leaving him unable to evade. Unwilling to lose the data he has gathered on Senketsu during their fight, Houka forfeits the match before Ryuko can destroy his uniform. Nonon steps up to battle Ryuko next with her Three-Star Goku Uniform, Symphony Regalia, a large aircraft that attacks her with sound vibrations. Nonon attempts to eliminate Ryuko by destroying the battle arena, but Ryuko activates a new aerial form, Senketsu Shippu, to remain in the match. Troubled by how quickly Senketsu has been evolving, Aikuro contacts Tsumugu and tells him to assume a worst-case scenario.

Ryuko tries to take advantage of her flight and go straight for Satsuki, but Nonon fiercely stands in her way until Ryuko destroys her airship with her own missile. However, Nonon puts on an encore performance unleashing her uniform's second form, Da Capo, using its music to disrupt Ryuko's communication with Senketsu. Ryuko counters this by manipulating Nonon's sound waves to match her own, before sending it back against Nonon and defeat her. Meanwhile, Tsumugu delivers a peculiar bullet to Aikuro, who is prepared to use it on Ryuko should the need arise. Just as Ryuko and Uzu are about to begin their match, a mysterious girl named Nui Harime appears between them, instantly pulling apart Uzu's uniform by breaking its Banshi, the Life Fiber that gives it its form. Nui then pulls out a purple scissor blade and reveals she was the one who killed Isshin, sending Ryuko into a fury.

As Ryuko angrily goes into a furious attack, Nui tells her how she killed Isshin with the Scissor Blades he himself created and stealing one of its blades, but not before having her left eye slashed in the process. The boiling blood of Ryuko's rage has an adverse effect on Senketsu, causing him to go berserk and consume her, resulting in a monstrous form. As Mako and her family head towards the scene in order to save Ryuko from dying of blood loss, Tsumugu tries to draw away Nui to give Aikuro the opportunity to use an adhesive bullet on Ryuko. Satsuki dons her Kamui in order to put a stop to Ryuko, but it is Mako who manages to slap Ryuko to her senses and bring her back to her normal self, saving her life. A few days later, as Ryuko is recovering from her battle, Satsuki reveals that she was the one who ordered Nui to steal the sword scissors from Isshin, before announcing that Ryuko's battles with the Elite Four have helped her perfect the Goku Uniforms so that they can take over every school that opposes them.

Satsuki prepares a raid on Osaka, Kyoto, and Kobe, issuing students with new Goku Uniforms created based on the data from Ryuko's battles. Meanwhile, Ryuko continues to sulk over losing control of Senketsu and is unwilling to wear him. She is approached by the suspended student and former Newspaper Club member Shinjiro Nagita, who pleads her to join the fight against Satsuki's war efforts, but she refuses. The next day, Mako gets roped into the raid trip for distributing Shinjiro's underground newspaper. Encouraged by Senketsu, Ryuko puts him on to help Shinjiro, who reveals himself to be a disguised Nui, having done so to trick Ryuko into donning Senketsu again. Unable to fight at her full strength out of fear of losing control again, Ryuko is defeated by Nui and Senketsu is torn to pieces. After Satsuki forces Nui to retreat, she takes all but one of Senketsu's scraps so that they may be distributed to suitable hosts to provide combat data during the raid trip.

Awakening in Aikuro's hideout, Ryuko discovers Senketsu's consciousness still lives in the scarf that she managed to hold onto. After learning what had happened to his other pieces, Ryuko heads towards the Kansai region, where Satsuki has begun her raid operation. As the Elite Four attack the main schools in the tri-city area, Ryuko interrupts each of their raids and recovers the scraps that had been given to some of the students to increase their power before heading to her next destination, eventually reuniting with Mako in Osaka. With nearly all of Senketsu's pieces gathered, Ryuko prepares to face Satsuki, who possesses the glove that makes up the final piece.

Satsuki confronts the money hungry boss of Osaka, Kaneo Takarada, who fights against her using his Dotonbori Robo suit. However, he is thwarted by the arrival of the Elite Four and their new Three-Star Goku Uniforms, before being promptly defeated by Uzu. Ryuko soon arrives on the scene to face against Satsuki, soon supported by the arrival of Aikuro, Tsumugu, and the Nudist Beach organization. While Nudist Beach fight against the Elite Four, Ryuko decides to use her own skin as a replacement for the glove so she can transform with Senketsu, allowing her to recover the glove from Satsuki. As Ryuko is disarmed of her scissor, Ryuko uses Senketsu to snatch Satsuki's sword from her, bringing the match to a stalemate. Ryuko coerces Satsuki into withdrawing her troops as opposed to simply killing each other, though Satsuki does fulfill her objective of destroying Nudist Beach's base. As Satsuki and her troops depart, Aikuro agrees to tell Ryuko everything she needs to know.

Satsuki returns to her mansion to recover from her battle with Ryuko. Impressed by her daughter's prowess with Junketsu, Ragyo shows Satsuki a chamber in their mansion containing the original Life Fiber, a parasitic extraterrestrial that produces other fibers to feed on mankind. She then instructs Satsuki to organize a school festival as the final step in her plan to distribute COVERS, an army of Life Fiber clothing, across the world. Meanwhile, Aikuro and Tsumugu guide Ryuko and Mako to an undamaged section of their underground base. Aikuro reveals that Life Fibers are what induced humanity's evolution into Homo sapiens and the instinct to wear clothes. He further explains that Isshin, who founded Nudist Beach, created Senketsu for Ryuko to wear and fight the Kiryuins when she came of age, as she displays a high resistance to Life Fibers. Ryuko becomes outraged that Nudist Beach sees Senketsu as little more than a weapon and takes him off, refusing to let him kill his own kind. Deeming them of no more worth, Tsumugu prepares to kill Ryuko and Senketsu.

After the fight between Ryuko and Tsumugu is dissolved thanks to Mako and Senketsu, Aikuro explains to her how Tsumugu's sister, Kinue, died in an experiment involving Life Fibers. Meanwhile, Honnoji Academy makes preparations for a Cultural and Sports Grand Festival to celebrate Ragyo visiting the school.

After freeing all the trapped students and citizens from the Life Fibers, the Elite Four fight against Nui while Mako helps with the evacuation.Meanwhile, Satsuki reveals how Ragyo had used her in Life Fiber experiments, along with her newborn sister, who was discarded by Ragyo when the experiment allegedly failed. However, Ragyo, who is able to heal her injuries, breaks free and takes control of the students, turning them into her personal army.

As the Covers start to kidnap citizens, including Mako, using their life force to power themselves, Satsuki triggers an explosion to allow Ryuko to escape. One month later, the Elite Four have joined up with Nudist Beach to fight against the Covers as they take over Japan, while Ryuko has remained in a coma since the battle. Meanwhile, Satsuki has been held captive by Ragyo, who explains that her father, Soichiro, had faked his own death and disguised himself as Isshin in order to raise Ryuko and prepare his revenge against her.

Paper clones of Ragyo and Nui appear before Ryuko, coaxing her into travelling to Honnouji Academy to confront them. Rejecting any help from the others, Ryuko heads off on her own. After hacking into Honnouji's security cameras and finding Satsuki's location, the Elite Four notice from Satsuki's actions that she is planning something. Their resolve renewed, they, along with the Mankanshokus and the rest of Nudist Beach, set forth on Aikuro's Naked Taiyoumaru warship and head towards Honnouji Academy to join the fight.

Satsuki and Senketsu begin their fight against Ryuko to try and bring her back to her senses, but they soon find themselves overwhelmed. The Elite Four soon join the battle, distracting Ryuko so that Ira can use his device to try and remove Junketsu. However, they are interrupted by Nui, who reveals that she has stitched Junketsu to Ryuko's Life Fibers, and forcibly removing it will kill her.

Ryuko reunites with Senketsu and fights against Nui, recovering both Scissor Blades and using them to destroy Nui's arms. Nui is rescued by Ragyo's secretary Rei Hououmaru, while the Elite Four and Nudist Beach take advantage of the Covers used for her escape to recover their allies and Life Fibers.

Ryuko and Satsuki arrive at the original Life Fiber to confront Ragyo, who now wields her own set of blades which prove resilient to their weapons. As the original Life Fiber turns it attack towards the ship, the Elite Four don new Goku Uniforms to assist Mako.

Ragyo uses her Shinra-Koketsu's Absolute Domination ability to negate the effects of everyone's Kamui and Goku Uniforms before reviving the original Life Fiber. Ragyo attempts to fuse everyone into the original Life Fiber, but Senketsu, who is immune to Ragyo's ability as he, like Ryuko, is neither human nor clothing, manages to knock Rei out of Shinra-Koketsu, negating its Absolute Domination ability and restoring everyone's power. This allows the Elite Four and Nudist Beach to destroy the satellite uplink while Ryuko and Satsuki deal a critical blow to Ragyo. However, Nui fuses herself with the original Life Fiber and combines with Ragyo, allowing her to launch into space so she can activate the satellite directly, where she begins her plan to convert the world into a Life Fiber coccoon. After promising to go on a date with Mako when she returns, Ryuko absorbs the combined power of Senketsu, Junketsu, and the Goku Uniforms to form Senketsu Kisaragi, launching into space and fight Ragyo, willingly taking her attacks to provide Senketsu with the power needed to absorb Ragyo's Absolute Domination ability and eliminate all of the Life Fibers, allowing humans to be humans. After Ragyo ends her own life, Senketsu uses the last of his strength and sacrifices himself to return Ryuko safely to Earth, where she reunites with her friends and family. With the world now free to wear what clothes they want, Ryuko goes on her date with Mako and Satsuki, keeping the memory of Senketsu in her heart.