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!

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!

Rinne, who is suffering, disappears from the presence of Houtaro and the others, and is kidnapped by Gaelijah along with Atropos.

Rinne's life will be in danger if nothing is done. Fuga and Glion, who has called for help, head for the rescue of Rinne and the others, only to find Gaelijah's evil trap awaiting them...!

And what about Houtaro, who arrives late to the scene!?