Novelist and bookstore owner Touma Kamiyama suffers a recurring dream about a place called Wonder World invading the real world and his inability to save a mysterious young girl named Luna 15 years prior. His dreams become reality when he is dragged into a war to decide the fate of both worlds, so he takes matters into his own hands when he obtains the means to transform into Kamen Rider Saber.

Touma is visited by a man from the Sword of Logos, Rintaro Shindo, who has come to relieve him of his SworDriver and Brave Dragon Wonder Ride Book. When Touma refuses to give them up, Rintaro takes him to his organization's headquarters to debrief him on the conflict he has become involved in. Touma now faces the choice of whether to use his power as Kamen Rider Saber to save people and the world, or stay out of it.

Touma meets two other members of the Sword of Logos. One is Kento Fukamiya, his childhood friend, and the other is Ryo Ogami, a great swordsman who divides his time between fighting and raising his son, Sora.

Despite Ryo defeating the Hanzaki Megid, the place it attacked did not return to normal and Sora is still missing. In response, Touma and the other members of the Sword of Logos look for a way to rescue him.

Touma and his friends must face Kamen Rider Calibur, a former member of the Sword of Logos who defected to the Megid's side. Meanwhile, Touma realizes that Kento is disturbed by the enemy's appearance and learns the connection between them.

Another member of the Sword of Logos, Ren Akamichi, visits Touma's bookstore seeking Kento's recognition. When he learns of Kento and Touma's friendship however, the young ninja develops a rivalry with the latter. Meanwhile, Megid commanders Storius, Legeiel, and Zooous make their move against the Sword of Logos.

Touma and Kento depart to look for the mythical land of Avalon so the former can unseal his sword, but Calibur stands in their way, intending to claim the secret power located there for himself.

After claiming the King of Arthur Wonder Ride Book and unsealing his sword, Touma begins to doubt if he can master the former's power. After Ryo is turned into stone while protecting him however, he comes up with an idea to rescue him with help from his friends.

After his recent feats, Touma is recognized by the others as a full-fledged member of the Sword of Logos, but when the Megids prepare multiple Alter Books for their next plan, Tetsuo Daishinji, the order's mechanic, joins the fray as Kamen Rider Slash after repairing his own weapon.

Calibur steals some Wonder Ride Books from the Sword of Logos to complete his plan. While fighting to get them back, Touma and his companions discover his true identity.

Touma and the others are shocked to discover that Calibur is Daichi Kamijo, the previous Kamen Rider Saber while Kento is in distress over not knowing his father's whereabouts. Meanwhile, the Megids strike again and Daichi appears with a new power that makes him a bigger threat.

After Rintaro is deeply wounded while protecting him from Daichi, Kento becomes determined to strike the enemy down not only for his sake, but also to avenge his father. Meanwhile, Touma and the others attempt to stop the Megids' plans.

Touma regains all his lost memories and realizes Daichi and the Megids' true objective, which is to recreate the same cataclysmic events of 15 years ago. Determined to stop them and avenge the fallen Kento, he obtains a new power.

While Touma defeated Calibur and foiled his plot, Kento has mysteriously disappeared. As the Megids continue to move forward with their own plans, the swordsmen head into battle against them with Kento's sword and Wonder Ride Books as well as a new power for Rintaro.

Touma dives into a portal opened by the pillars of light to stop Calibur while the other swordsmen look for a way to close it despite being warned by the Megids that Touma will not be able to return if they do so.

After defeating Calibur and averting the latest crisis, Touma prepares to celebrate the new year with his friends. However, Sword of Logos member Reika Shindai manipulates the others into believing that Touma is a traitor and turns them against him. While on the run, Touma encounters a man named Yuri, who reveals himself as the Light Swordsman, Kamen Rider Saikou.

Touma is on the run from the Sword of Logos, who have branded him an enemy. However, when the Megids discover a way to turn humans into monsters, a conflicted Touma faces the possibility of killing an innocent to stop the Megids' plans.

Touma looks for a way to defeat the Yeti Megid without killing its human host, though Yuri is certain that she is beyond salvation. Meanwhile, the other swordsmen start having doubts about Reika's accusations against Touma.

Several people are disappearing and Reika insists that Touma is involved in it, ordering the other swordsmen to fight him. While Touma and Yuri conduct their own investigation into the matter, the Megids turn another person into a monster.

Following his duel with Touma, Tetsuo informs his fellow swordsmen that the Megids have discovered a way to turn humans into monsters, but Reika deflects the issue by telling Ren that Touma still has Kento's sword. Amidst the incensed ninja's attempts to take his idol's sword back from him and attacks by the Megid warrior Desast, Touma attempts to help the Megids' latest victim, who keeps changing back and forth between his human and monstrous forms.

Touma and Yuri continue looking for the people who disappeared. While Yuri decides to regain his lost powers as a swordsman, Tetsuo confronts Touma directly to test if he is capable of unlocking the true power of the Kaenken Rekka.

After rescuing a young woman from the Charybdis Megid, Touma learns that her sister is still missing. Fearing that she is still under the Megids' influence, Touma looks for her, but Ryo stands in his way in another attempt to confiscate his swords and Wonder Ride Books.

To set things straight with the Sword of Logos, Touma decides to break into Southern Base to meet their leader, the elusive Master Logos. Little does he know that Storius also intends to invade it to claim the organization's forbidden tome. In the chaos of battle, Touma ends up acquiring the tome, which transforms into the unstable Primitive Dragon Wonder Ride Book. Possessed by its overwhelming power, a feral Touma viciously defeats Legeiel in combat before collapsing from exhaustion.

Both Touma's allies and enemies are astonished by the unknown and uncontrollable power of Primitive Dragon. Reika orders Rintaro to steal the book from Touma, even if he needs to kill him, but Ryo decides to finally confront Reika about her true intentions. In the midst of this, a new Calibur enters the fray to save Touma from Primitive Dragon's influence.

Touma desperately looks for a way to contain the overwhelming power of Primitive Dragon before he ends up killing someone. Meanwhile, Reika grows tired of Ryo and Tetsuo's disobedience and decides to use her own powers as a Kamen Rider to eliminate them.

Much to everybody's surprise, Kento reappears and assumes his father's mantle as Kamen Rider Calibur, affirming that the only way to protect the world from destruction is by sealing all the sacred swords. Despite Kento's decision, Touma attempts to reason with him, only to learn the harsh truth behind his motives.

Touma attempts to rescue the boy he saw in his dreams from the deep sadness he is engulfed by. Meanwhile, Legeiel evolves into a new and powerful form, determined to have his revenge against Saber. In the midst of their fight, Touma learns the boy is a physical representation of Primitive Dragon who had lost all of their friends. Touma befriends it, promising he will never abandon it. In the process, he tames Primitive Dragon and acquires the Elemental Dragon Wonder Ride Book. Combining the two books, Touma transforms into Saber Elemental Primitive Dragon and destroys Legeiel, freeing his human soul.

Ren leaves the Sword of Logos, determined to join forces with Kento. However, the latter decides to not accept Ren's help and proceeds to seal his sword instead when Touma appears to stop him.

Rintaro decides to confront Master Logos for the truth about his intentions, but must first contend with his leader's right hand Ryoga Shindai, aka Kamen Rider Durendal.

Having discovered the truth about Master Logos, Rintaro rejoins Touma and the other Northern Base swordsmen. Seeing this, Mei considers how she can contribute to their fight. However, the Megids turn her into a monster bent on destroying Rintaro. Upon discovering this, Rintaro and Touma are faced with the dire crisis of whether they can save her or not.

An ashamed Rintaro flees from the Northern Base after failing to protect Mei from the Megids. Faced with the fear of losing his friend, Touma confronts the enemy alone to rescue her, but Zooous stands in his way to prevent him.

After saving Mei, Rintaro's confidence is restored. However, Master Logos destroys the barrier protecting the Northern Base, leading to the Shindai siblings and the Megids launching simultaneous attacks on it. The remaining Northern Base swordsmen are forced to split up to tackle these situations, with Touma and Yuri fighting the Shindais while Rintaro and Ryo battle the Megids. Taking advantage of the siege, an evolved Zooous intends to settle his rivalry with the former. However, Rintaro gains the Tategami Hyoujuu Senki Wonder Ride Book from the Northern Base's Tome of Omniscience and transforms into his strongest form yet to defeat Zooous once and for all.

Despite Rintaro's new power, Reika succeeds in stealing Ryo and Tetsuo's swords as well as Kento's original sword as Master Logos' plan calls for all of the Riders' swords to be gathered. While the swordsmen move to protect Ren, Touma approaches Kento and attempts to convince him to return to the Northern Base. However, Kento reveals he saw visions of the world's destruction and of Touma dying while saving it, along with his determination to avert these possible futures. Suddenly, Master Logos appears before the duo, determined to steal their swords himself.

Touma and the others rejoice upon learning that Luna is still alive, but Master Logos uses the Book of Ruin to revive the Immortal Swordsman, Bahato, and sends him to fight the Northern Base swordsmen once more.

While protecting Touma from Kento and Bahato, Yuri vanishes. Luna appears during the battle, but is kidnapped by Reika, who prepares the stolen swords and Wonder Ride Books for a ritual that will allow Master Logos to become a god. After fainting from his injuries, Touma witnesses his friends locked in battle against Master Logos and Bahato and attempts to join them. In the process, he reacquires the Emotional Dragon Wonder Ride Book and uses it to defeat Bahato.

Having reclaimed their swords and books thanks to Touma, the swordsmen and a revived Yuri join forces to rescue Luna and stop Master Logos' plans. Meanwhile, Reika and Ryoga learn their master's true colors and decide to oppose him. Ultimately, the swordsmen succeed in saving Luna, interrupting the ritual, and regaining their powers, with Kento choosing to retain the Calibur title instead of re-taking up the Raimeiken Ikazuchi to honor his father's legacy. However, their victory is short-lived when Logos succeeds in obtaining the Caladbolg sword, the Omni Force Wonder Ride Book, and his own Rider powers.

Isaac, formerly Master Logos, declares war on humanity and sets out to refine his already incredible power further. To stop him, Kento is determined to sacrifice himself in Touma's place. Touma and Rintaro attempt to stop him, but Ren appears in their way, challenging the former to a duel.

Despite the united swordsmen's best efforts, Isaac continues his plot to destroy the world, causing them to look to Touma for answers. Meanwhile, Touma prevents Kento from sacrificing himself and hands him his original sword, but Kento refuses to use it. Suddenly, Bahato challenges Touma once more, but the latter acquires a new power that just may turn the tide of battle in his and his allies' favor.

After receiving Luna's help in creating the Haouken Xross Saber, Touma has destroyed Isaac's books and restored sections of the city previously thought to have been gone forever. However, Isaac continues to further his plans, leading to the possibility that he wanted Touma to create the new Seiken. Meanwhile, despite fighting Isaac alongside the Northern Base swordsmen, the Shindais, Ren, and Kento decide to forge their own paths independently of them.

Using Omni Force's ability to control Wonder Ride Books, Isaac takes control of Ryoga via his book and forces him to attack Reika. Isaac then targets Luna once more due to her connecting Earth to Wonder World despite Tassel's best efforts to protect her. Touma, Rintaro, and Kento unite to protect Luna and defeat Isaac for good. However, Storius takes advantage of the situation to personally kill the former Master Logos and steal the Omni Force Wonder Ride Book for himself.

Isaac has fallen, though Storious has taken over their plan to end the world while Desast opposes him. Meanwhile, Tassel appears before Touma and the swordsmen to reveal the origins of Wonder World, the Megids, and the Almighty Book in order to influence how Touma will decide his story's ending.

Touma learns he is slowly vanishing as a result of his increasing power as Saber, which aligns with one of Kento's visions. Despite this, the latter continues on, intending to determine his story's ending himself. To do so, he needs Luna, who Tassel has been searching for, only to encounter Storious instead. Meanwhile, Ren continues his search for true strength while Desast, having become immortal after assuming Bahato's Rider powers, challenges Touma to a duel.

After killing Tassel and stealing his book, Storious begins a ritual to restore the Tome of Omniscience before he begins destroying Earth and Wonder World. Touma and the swordsmen succeed in slowing the Megid's progress, but a prophecy reveals Touma is necessary for Storious' plans. Despite this, Touma works to recover Tassel's book and stop Storious. Meanwhile, Ren accepts Desast's challenge for a duel.

Storious creates the Grimoire Wonder Ride Book using Legeiel, Zooous, Isaac, Tassel, and Charybdis' powers along with the Tome of Omniscience and reanimates the Sword of Logos' Four Sages to serve him. Meanwhile, despite struggling to stop Wonder World's collapse, Touma and his fellow swordsmen must face Storious if they hope to save the world.

As Storious' plan progresses and Wonder World and Earth collapse, the swordsmen are unexpectedly joined by Sophia as the latest Calibur as well as Luna and Mei. With their forces bolstered, the swordsmen face Storious and his army.

One by one, the swordsmen fall for one reason or another as Storious overwhelms them. Touma attempts to face him alone, but learns a horrible truth regarding the Almighty Book. Meanwhile, as Wonder World vanishes and Earth collapses, a vanishing Mei reaches a decision as she attempts to reach a similarly vanishing Luna.

Luna sacrifices herself to give Touma and his friends the power to defeat Storious. While they fail to stop the destruction of Earth and Wonder World, Mei's initiative and his readers inspire Touma to bring forth a miracle.

After saving Earth and Wonder World together, Touma and his friends enjoy a well-deserved rest and begin to go their separate ways. However, their peaceful days are interrupted by a strange monster they have never encountered before known as a Deadman along with a boy and his demon partner capable of transforming into Kamen Rider Revice, accompanied by their associate George Karizaki, who are hunting the cult the Deadman belongs to.