Houtarou is a high school student in search of his own "Gotcha" (something unique to him). However, he is still in a daze, unable to even decide on a career path. His classmate Rinne looks down on him. Then, Houtarou meets a grasshopper. "I don't know what it is, but when I'm with you, I feel a stirring in my heart..." Then, Steamliner suddenly appears and takes Houtarou to another space. In the other space, a mysterious man entrusts Houtarou with a Driver, saying it is his hope for the future. Then an enemy attacks! The target is Houtarou's Driver. Houtarou loads the card into the Driver! He transforms into Kamen Rider Gotchard..!

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...!