Kaguya, who is reunited with Houtaro, comes to Furasu High School and charms the students with his "gorgeousness." Houtaro is taken aback by the notoriety that even a fan club has been formed. Houtaro and Kaguya are again faced with the appearance of the Hundred's Kasshine army. Houtaro and the others transform into Riders and defeat them, but Kaguya utters ominous words about the leaders still being nearby...?!

Kaguya transforms into Legend and attacks Houtaro. Houtaro also transforms into Gotchard and fights back, but Kaguya shuts him down and says, "Gorgeous time is over," and leaves him alone. They are supposed to have made up, but why? Houtaro and the others are puzzled by Kaguya's sudden change, but then a giant clock appears in the sky above them. What does the ticking of the clock mean? Moreover, the Dark King Gigist begins to act in secret...!?

Houtaro and others show Kyoka the completely white Skebows. They want to somehow regenerate Skebows! Houtaro and the others look at it as if praying, and Kyoka...!? Hopper1 sets off alone on a journey to find "something" to cheer up Houtaro. Meanwhile, Gigist has taken Antrooper from Houtaro and turned it into a Malgam. The Malgam attacks people, and Houtaro and the others...!?

Houtaro, who was spirited away from Rinne and the others by a giant egg, finds himself in a black space with a floating blue egg. "What is this place? Who are you?" Houtaro asks the egg. Gigist stands before Supana, who was on his way to rescue Houtaro. Supana transforms into Kamen Rider Valvarad, only for Gigist to unleash the mighty Malgam, which he had created by rallying his Chemies, on Kamen Rider Valvarad!

Supana summons Houtaro and the others, erases the Chemy Cards so that they cannot be re-sealed again, and takes all the Chemy Cards from Houtaro and the others. However, Kyoka and Lachesis appear and reveal Supana's true intentions in front of Houtaro and the others. When Houtaro learns the horrifying truth about Supana, he approaches Supana with fury. "Why are you always like this?" Houtaro and Supana finally clash!

Rinne, who is suffering, disappears from the presence of Houtaro and the others, and is kidnapped by Gaelijah along with Atropos. Rinne's life will be in danger if nothing is done. Fuga and Glion, who has called for help, head for the rescue of Rinne and the others, only to find Gaelijah's evil trap awaiting them...! And what about Houtaro, who arrives late to the scene!?

Houtaro, who defeated the Malgam and got a new Chemy, was attacked by an angry Clotho! With Geryon gone, what is the point of fighting? Houtaro fights back and pleads desperately, but Clotho refuses to listen to him. Then, suddenly something unusual happens and a new enemy appears to attack Houtaro and the others...!?

Mami, the director of Kongo Laboratory, begs Houtaro and the others to protect the laboratory from Geryon. Protect it from Geryon? What is the relationship between Mami and Geryon...? Houtaro, suspicious of the Chemy's behavior, asks Sabimaru if it was really Kenichi who created the Chemy. For a moment, Sabimaru is perplexed, but then he reveals the truth behind the Tsuruhara brothers and Chemies. What is that unexpected truth!?

Gotchard defeats the Malgam, who threatens the people, but the people of the city still fiercely condemn Chemies and the alchemists. A world where people and Chemies can live together.... Houtaro has no end to his worries. Supana has lost his driver, and Gigist calls on him to fight with him. Supana refuses, and fights as Valvarad, but is engulfed by the black flames that Gigist unleashes. Supana foresees his own demise... but then!?

Glion, transformed into Kamen Rider Eld by the power of the Philosopher's Stone, summons an army of Dreatroopers. The city and its people are transformed into gold, and El Dorado is steadily approaching completion. Houtaro tells his mother, Tamami, that as a Kamen Rider he will create a future where humans and Chemies can live together, and that he doesn't want to run away from his Gotcha! He then joins Rinne, Supana, and the other Chemies in a final battle to defeat Glion!

"Kudo! Fight like you are!" With the advice of Minato, Houtaro and Rinne manage to escape their predicament, but Rinne's feelings and the future of the "Romeo and Juliet" production become uncertain. Furthermore, Atropos appears with a new Malgam. Houtaro and Rinne transform into Riders, but Majade strikes them with a powerful blow...!

Houtaro and his team receive information that the 102nd Chemy has unexpectedly appeared. Houtaro, Supana, and Sabimaru begin a search based on this information, and arrive at a certain research institute where Sabi's brother, Ken'ichi, works. A new Malgam appears at the institute. Is the 102nd Chemy real after all? And behind it all is the resurrected Geryon!? Houtarou and Supana transform into Riders...!

When Hijiri is brought to Gaelijah, she is shocked to discover that she has been transformed into a Malgam herself. Gaelijah tries to release her despair and transform her back into a Malgam. Houtaro and Kajiki arrive on the scene. Houtaro transformed into Gotchard and entrusted Kajiki with rescuing Hijiri, but for some reason Hijiri shuns Kajiki, saying, "Don't come!" And Kajiki shuns her...!?

Seeking the teachings of Renge and Sabimaru who has sealed away a lot of Chemies, Houtarou and Rinne go to a certain professional wrestling Dojo with Renge and the others. When Houtarou immediately tries to find a Chemie, he's attacked by gang-like men who are after the Dojo's land. However, Alchemy can't be used against ordinary people. In front of a confused Rinne and the others, Houtarou borrowed Renge cards and transformed into Gotchard! However this time, a powerful Malgam suddenly appears!

"There's something I'd like to ask of you, Ichinose." Houtaro is asked by Rinne, who has a thoughtful look on her face, to confide in him about a certain problem of hers. Just what exactly is on her mind? Then the two are dispatched to the appearance of a new Level 10, X-Rex. Houtaro and Rinne attempt to tame it but encounter a little girl instead...

People's memories come back and information spreads that Chemies are terrifying entities that turn humans into monsters. The town is in a state of panic, filled with people who fear Chemies and Malgams, and those who want to obtain Chemies and use them for evil purposes. Then, Golem Gouriki appears before Houtaro and transforms into the Gorilla Malgam. The alchemists are accused of being the masterminds behind the series of disturbances. If nothing is done, the world will be in chaos... Supana makes a decision and takes action!

Hijiri, whom Kajiki is in love with, has a boyfriend! Although Kajiki is depressed, he learnt that Hijiri boyfriend is most likely the remaining suspect who made his escape after Clotho attacked the police van! If that's the case, then there's a possibility that the suspect has already became a Malgam. Hijiri who is with Kajiki is in danger! Houtarou and Minato start searching for the suspect together, but...!

The village chief is found in a grisly state, and the villagers assume it is the work of Starshine Hoshino and make a big fuss. They lock Hoshino and his apprentice Kajiki in a warehouse. Kajiki would never attack anyone. As Houtaro and the others begin their search for the real culprit, a new Malgam appears. Houtarou transforms into Gotchard, but he feels something strange about the Malgam's behavior. What is this discomfort? And what is the truth behind the incident...!?

In order to save the drama club, Houtaro and his friends decide to help put on a performance of "Romeo and Juliet". Mikuriya, the head of the club, selects Houtaro to play Romeo, while Seina, a transfer student and childhood friend of Houtaro, runs for the role of Juliet, while Rinne is put off by the fact that she is not a member of the club. Rinne is bothered by Houtaro and Seina's sudden closeness. Atropos appears, sees through Rinne's emotional turmoil, and unleashes a Malgam. Rinne desperately defends Seina who is nearby...!

The Dark King Gigist appeared at the Union headquarters. Supana, angered by Gigist's defeat of one of the Union leaders, transforms into Kamen Rider Valvarad. He boldly attacks Gigist, but... Gigist appeared in front of Houtaro, took away Skebows' card, and turned it into a Malgam. Houtaro transforms into Gotchard and challenges the Malgam to save Skebows, but he feels something strange in the battle...!?

Renge proposes a competition to retrieve the two remaining Chemies, with Nijigon at stake. Despite a stunned Houtaro, Rinne, Sabimaru, and even Nijigon get involved...! Gigist appears before Houtaro. Gigist tries to dye the Chemies in darkness, but Houtaro uses the power of Nijigon to prevent him from doing so. He transforms into Rainbow Gotchard and clashes with Gigist!

It was the Underworld King Germain and Gaelya who descended to earth from the Ouroboros world. Their target is Fuga, the father of Rinne, the most powerful alchemist. The Three Dark Kings, including Gigist, are closing in on Fuga. Houtaro, Rinne, and Supana rush to the scene and transform into Riders! They confront the Dark Kings to protect Fuga, but they are cornered by the unprecedentedly vicious power used by Germain and the others...!

While Houtaro and the others continue their search, Nijigon is wandering the streets, refusing to return until he finds something he can do to help. Nijigon meets a woman practicing dance. Germain appears before Houtarou and the others again. Together with Rinne and Supana, they transform into Riders and face Germain with a strong determination to defeat him!

After transforming into Kamen Rider Gotchard, Houtarou wants to learn more about the Chemmies and is advised by his teacher Minato to take the entrance exam for the secret Alchemy Academy. However, Houtarou runs into a problem. Meanwhile, Ryo Kajiki meets a talking skateboard who loves to play with children, but...

Houtarou and his group from Furasu High School go on a school trip to Kyoto. Houtarou is assigned to a group study with Rinne and Kajiki, and by chance Kajiki meets a girl named Hijiri, and they hit it off. They immediately become attracted to each other. At the same time, one of the Three Dark Sisters, Clotho, was also sighted in Kyoto in order to obtain something. But Clotho happens to see Houtarou and the others, and in her anger, she creates a new Malgam...!