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 Chemies and is advised by his teacher Minato to take the entrance exam for the secret Alchemist Academy. However, Houtarou runs into a problem.
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 have 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.
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?" 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.
Hijiri, whom Kajiki is in love with, has a boyfriend. Although Kajiki is depressed, he learnt that Hijiri's boyfriend is most likely the remaining suspect who made his escape after Clotho attacked the police van.
Clotho captures a new Chemy, UFO-X, in Kyoto. It seems that it has something to do with the mysterious driver that the Three Dark Sisters are plotting - Meanwhile, Houtarou and his friends continue to work hard to recover Chemies.
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.
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.
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.
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.