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.