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 continues his quest to befriend all the Chemies as he meets a Chemy known as Apparebushido, and is given his card by Minato. A new Malgam appears and Houtarou attempts to fight it using Apparebushido, but it defies orders and causes Houtarou to be defeated. "Just how can I get Apparebushido to open up to me?" Houtarou asks himself as he begins to secretly train. Just then, he is approached by alchemist named Spanner Kurogane, who demands the Gotchardriver!

Houtarou can't help but exclaim in admiration at Valvarad's powerful might. However, Spanner says that he didn't acknowledge Houtarou as a Kamen Rider and leaves. Houtarou and Rinne, who continue their search for Chemies, come face to face with the Three Dark Sisters, Atropos, Clotho and Lachesis. Lachesis then absorbs a Chemy and transforms into Malgam. Houtarou transforms into Gotchard, but immediately after that, they are sent to a huge, different space!

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!

A mysterious man appears in front of Supana after tracking him. He changes into a Malgam before attacking the former and Houtarou. Supana then transforms into Valvarad and counters, and so does Houtarou into Gotchard, but the Malgam escapes after Valvarad's counterattacks. However, the man, who is set on overthrowing Supana, kidnaps Rinne in front of Houtarou in order to lure his nemesis out. Who on earth is this man? And why is he so obsessed with Supana!?

A boy appears in front of Houtarou and others, asking to take over Saboneedle. Since Ordinary people and Chemies cannot coexist, Rinne, who values the rules, tries to accept the boy's request, but Houtarou is not convinced. Doesn't he really want to be with Saboneedle? Houtarou tries his best to find out the boy's true feelings, but then a new Malgam appears. What is the true identity of Malgam who is targeting the boy for some reason!?

Saboneedle flew out of the driver during the battle with Dragonfly Malgam. Houtarou senses something as Riku becomes more distraught than ever, asking, "Where has Sabosuke gone?" Meanwhile, Atropos suddenly appears in front of Rinne...!

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...!

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...!

Clotho captures a Level 10 Chemy for the Three Dark Sisters and subjects it to their creepy experiments, bringing them closer to completion of "something". Meanwhile, Kugimiya and Harima from the Alchemys Union arrive at the academy and warn the students that there may be a mole within their ranks. However before he begins investigating on who the possible mole is, he heavily criticizes Houtarou's fighting style as a Kamen Rider.

The spy for the Three Dark Sisters turned out to be Shiori Harima, an investigator from the Alchemy Union. Houtarou lashes out in anger at Shiori, who attacks the Chemy, but is tormented by her use of forbidden alchemy. Then the Three Dark Sisters appear. When Atropos and her sisters get their hands on a mysterious driver, they say "now it's your turn" to the mysterious warrior known as Kamen Rider Dread, and begin a new terrifying experiment. Just who is this dark destroyer, Dread?

"Sabimaru-Senpai is gone." Houtarou laments his immaturity and weaknesses in the face of fleeting, yet endless suffering. How can he help Sabimaru? Just then, Houtarou is invited by Kajiki to call out a UFO whose sighting has recently become more frequent. Houtarou and his friends find a possibility to rescue Sabimaru by befriending UFO-X. However, the Three Dark Sisters and Sabimaru with the Dreadriver appear before them! Equip yourself with the Number 10 Chemy and Change to Super Gotchard now, Houtarou Ichinose!

"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...

The raw power of Super Gotchard overwhelms Dread and gains an upper-hand, but Dread is capable of executing counterattacks, resulting in a back-and-forth battle. Meanwhile, Lachesis approaches the daughter-father duo Sawa and Manabe. Rinne attempts to protect them but Atropos intervenes with her magical abilities. "So you are powerless after all." Rinne is robbed of her bodily freedom by the triumphant Atropos...?!

Supana returns to his master Kyoka Edami to have her repair his Valvarusher, which was heavily damaged during his battles with the Three Dark Sisters. As he arrives in her laboratory, he becomes intrigued by the blueprints of a new weapon she is developing. A giant snake suddenly appears from the sky and attacks people with its petrification rays. Houtaro transforms into Gotchard and confronts the snake, who speaks in an eerie voice. "Are you Kamen Rider...?" What is the true identity of the giant snake?

While Houtarou is serving New Years Food to Rinne and the others, he's wondering who is the Orange Gotchard that appeared during Christmas, and the sudden strengthening of the Malgam... Suddenly, a Malgam appeared before Houtarou! Houtarou transformed into Gotchard, but he struggled against the empowered Malgam. As the Orange Gotchard appeared, he tells the shaken young man "As you are right now, you'll never defeat that Malgam." A suprising development awaits Houtarou and co. as a person starts to move after Geryon's revival...

Houtaro and Rinne are disappointed in a world where not only the Alchemy Academy, but also their teacher Minato does not exist. The Moon Malgam then appears in front of the two and mocks Rinne where it takes her into the shadows. "What should I do to become stronger and defeat the Moon Malgam?", asks a worried Houtaro. Gotchard Daybreak then replies. "I will transport you to the past." Just what is in Houtaro's past? What should he do there?

Houtaro and his friends are in high spirits once they formed the Kitchen Ichinose Alliance. However, Rinne is still dispirited as she wonder if this is the 'rules' she had to follow as an alchemist. While Rinne is elated to know that Fuga is in fact not a traitor at all, Minato suddenly comes to her and invited her back into the academy! While this might be the right thing to do as an alchemist, Rinne is shaken by her former teacher's invitation. Meanwhile, Atropos arrives with a new Malgam and ordered the Malgam to exclusively attack Rinne. With Gotchard struggling, Rinne is cornered! What did she see in Atropos? Now, the sleeping power inside of Rinne will be awakened! Now transform into Majade, Rinne Kudo!

Kyoka arrives to see Houtaro and the others. Kyoka, who claims to be Supana's teacher, begins to talk about Supana's past, which even Houtarou and the others did not know. "It all started 10 years ago..." At that time, Supana's parents appear before him, worried that he will never be as strong as Houtaro and Rinne. Supana is happy to see his parents again after a long time, but...!?

Houtaro drives the runaway Wheel Malgam into de-transformation with the power of Fire Gotchard. However, Supana stubbornly shuts his mind, saying to Houtaro and the others, "This is my battle," and remains engulfed in black flames. Houtaro and the others support Kyoka in making a new driver for Supana. They continue working on it through the night, but now Geryon's evil hand is closing in on Kyoka..!

Renge has fallen under the spell of Zukyumpire. Zukyumpire attracts many men and women, but when Houtaro and his friends investigate, they discover that Renge and the others are in danger...!? Meanwhile, Geryon, who has failed to dye Supana with malice, begins a new course of action using Clotho!

Houtaro and Rinne try to stop Zukyumpire, who steals energy from people. Then, Renge and others bring one of the Zukyumpire worshippers, Yui, to the scene. Houtaro and the others, after hearing from Yui about the circumstances surrounding Zukyumpire, desperately try to persuade him. When Zukyumpire learns that he has been tormenting people, he is devastated, and at the same time, something strange happens around him. At the same time, strange happenings occur around them, and Clotho shows up to take advantage of them..!

Houtaro and the others are overjoyed to receive a letter from Minato saying that he will take down Geryon. They immediately rush to the location Minato has designated, but suddenly a new Malgam appears. Houtaro is deprived of all his cards except for Steamliner. He is unable to transform into Gotchard. Houtaro still wants his cards back, so he consults with Kyoka and learns that there is only one way to transform, though it is a forbidden technique...

Houtaro transforms into Iron Gotchard, but his physical strength is depleted and the transformation is canceled. He is saved by Fuga, the father of Rinne, who suddenly appears and escapes from the battle with Dread Type One. Fuga explains about "an incident" that occurred 10 years ago, which is the reason why Minato abandoned Houtaro and the others to follow Geryon. Houtaro and the others, who understand Minato's true intentions, confront him once again...!

Geryon has unleashed the deadliest Malgam to open the door to darkness. Rinne and Supana transform into Riders to face him, but they are cornered by his powerful force. Houtaro transforms into Iron Gotchard to save them. They go head-to-head, but gradually his strength is depleted and he is unable to transform. Just when all seemed to be lost, Fuga appears. "I will light the way for these youth." And then Fuga...!

Houtaro, Rinne, and Supana transform into Riders in front of Geryon, who tries to open the dark door! Geryon also transforms into Dread and tries to steal the Gotchardriver. However, Iron Gotchard soon reaches the limit of his strength and is attacked by Dread, causing him to untransform. Geryon gets the Gotchardriver and finally opens the door to darkness...!?

Renge, who was visiting her grandmother's village, informs Houtaro and the others that a yokai has appeared and she wants them to come immediately. In that village, a man named Starshine Hoshino, who calls himself a specialist in exterminating yokai, appears, and his apprentice is Kajiki!? Houtaro and Rinne arrive in the village and immediately discover the yokai! Houtaro transforms into Gotchard...!

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...!

"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, 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...!?

Saigetsu, Mimei, and Tasogare of a mysterious organization appear before Houtaro and the others. The three, who say they are looking for a super weapon in this world, call in the Kasshine army to attack the people. We will stop them! In front of Houtaro and the others, who are furious, Saigetsu and the others transform into Kamen Riders such as Dark Kiva! Houtaro, Rinne, and Supana also transform into Riders and stand up to them...!

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...!?

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...!?

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!

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!

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...!

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!?

Kajiki is depressed after being cold-shouldered by Hijiri, but is beginning to remember the memories that have been erased by Minato. Houtaro suggests to Minato that he revive all of Kajiki's memories for Kajiki and Hijiri's sake, but... Meanwhile, the Dark King Gaelijah had begun a new course of action using Clotho. And that Malgam is in front of Houtaro and Rinne!?

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...!?

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!

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!?

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!