A man appears with a spanner in his hand. The man transforms into a Malgam in front of Supana and Houtarou and attacks Supana. Supana also transforms into Valvarad and counters, Houtarou also transforms into Gotchard, but the Malgam is attacked by Valvarad and escapes. However, the man, who is obsessed with overthrowing Supana, kidnaps Rinne in front of Houtarou in order to lure Supana out. Who on earth is this man? And what is the reason for aiming Supana!?

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. When Houtarou immediately tries to find a Chemy, 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!

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 Chemy, comes 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!

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!

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. Meanwhile, Ryo Kajiki meets a talking skateboard who loves to play with children, but...

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..!