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.
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.
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.
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..
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.
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.
Houtaro drives the runaway Wheel Malgam into de-transformation with the power of Super Gotchard. However, Supana stubbornly shuts his mind, saying to Houtaro and the others, "This is my battle," and remains engulfed in black flames.
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.