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.

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.

Houtarou continues his quest to befriend all the Chemies as he meets a Chemy known as Apparebushido, and is given his card by Minato.

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.

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.

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.

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.

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?"

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.

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!

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".

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.

"Sabimaru-Senpai is gone."

"There's something I'd like to ask of you, Ichinose."

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.

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.

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...

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.

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.

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..."

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.

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...!?

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 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.

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.

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, 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.

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!?

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.

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.