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.

A giant snake suddenly appears from the sky and attacks people with its petrification rays. Houtaro transforms into Gotchard and confronts the snake, who speaks in an eerie voice.

"Are you Kamen Rider...?"

What is the true identity of the giant snake?

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...

Suddenly, a Malgam appeared before Houtarou! Houtarou transformed into Gotchard, but he struggled against the empowered Malgam. As the Orange Gotchard appeared, he tells the shaken young man "As you are right now, you'll never defeat that Malgam."

A suprising development awaits Houtarou and co. as a person starts to move after Geryon's revival...

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.

"What should I do to become stronger and defeat the Moon Malgam?", asks a worried Houtaro.

Gotchard Daybreak then replies. "I will transport you to the past."

Just what is in Houtaro's past? What should he do there?

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!

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..."

At that time, Supana's parents appear before him, worried that he will never be as strong as Houtaro and Rinne. Supana is happy to see his parents again after a long time, but...!?

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.

Houtaro and the others support Kyoka in making a new driver for Supana. They continue working on it through the night, but now Geryon's evil hand is closing in on Kyoka..!

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...!?

Meanwhile, Geryon, who has failed to dye Supana with malice, begins a new course of action using Clotho!

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, after hearing from Yui about the circumstances surrounding Zukyumpire, desperately try to persuade him. When Zukyumpire learns that he has been tormenting people, he is devastated, and at the same time, something strange happens around him. At the same time, strange happenings occur around them, and Clotho shows up to take advantage of them..!

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.

He is unable to transform into Gotchard. Houtaro still wants his cards back, so he consults with Kyoka and learns that there is only one way to transform, though it is a forbidden technique...

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.

Fuga explains about "an incident" that occurred 10 years ago, which is the reason why Minato abandoned Houtaro and the others to follow Geryon. Houtaro and the others, who understand Minato's true intentions, confront him once again...!

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 transforms into Iron Gotchard to save them. They go head-to-head, but gradually his strength is depleted and he is unable to transform. Just when all seemed to be lost, Fuga appears.

"I will light the way for these youth." And then Fuga...!

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.

However, Iron Gotchard soon reaches the limit of his strength and is attacked by Dread, causing him to untransform. Geryon gets the Gotchardriver and finally opens the door to darkness...!?

"Kudo! Fight like you are!"

With the advice of Minato, Houtaro and Rinne manage to escape their predicament, but Rinne's feelings and the future of the "Romeo and Juliet" production become uncertain.

Furthermore, Atropos appears with a new Malgam. Houtaro and Rinne transform into Riders, but Majade strikes them with a powerful blow...!

While Houtaro and the others continue their search, Nijigon is wandering the streets, refusing to return until he finds something he can do to help. Nijigon meets a woman practicing dance.

Germain appears before Houtarou and the others again. Together with Rinne and Supana, they transform into Riders and face Germain with a strong determination to defeat him!

Houtaro and his team receive information that the 102nd Chemy has unexpectedly appeared. Houtaro, Supana, and Sabimaru begin a search based on this information, and arrive at a certain research institute where Sabi's brother, Ken'ichi, works.

A new Malgam appears at the institute. Is the 102nd Chemy real after all? And behind it all is the resurrected Geryon!? Houtarou and Supana transform into Riders...!

Mami, the director of Kongo Laboratory, begs Houtaro and the others to protect the laboratory from Geryon. Protect it from Geryon? What is the relationship between Mami and Geryon...?

Houtaro, suspicious of the Chemy's behavior, asks Sabimaru if it was really Kenichi who created the Chemy. For a moment, Sabimaru is perplexed, but then he reveals the truth behind the Tsuruhara brothers and Chemies. What is that unexpected truth!?

Kajiki is depressed after being cold-shouldered by Hijiri, but is beginning to remember the memories that have been erased by Minato. Houtaro suggests to Minato that he revive all of Kajiki's memories for Kajiki and Hijiri's sake, but...

Meanwhile, the Dark King Gaelijah had begun a new course of action using Clotho. And that Malgam is in front of Houtaro and Rinne!?

When Hijiri is brought to Gaelijah, she is shocked to discover that she has been transformed into a Malgam herself. Gaelijah tries to release her despair and transform her back into a Malgam.

Houtaro and Kajiki arrive on the scene. Houtaro transformed into Gotchard and entrusted Kajiki with rescuing Hijiri, but for some reason Hijiri shuns Kajiki, saying, "Don't come!" And Kajiki shuns her...!?

People's memories come back and information spreads that Chemies are terrifying entities that turn humans into monsters. The town is in a state of panic, filled with people who fear Chemies and Malgams, and those who want to obtain Chemies and use them for evil purposes.

Then, Golem Gouriki appears before Houtaro and transforms into the Gorilla Malgam. The alchemists are accused of being the masterminds behind the series of disturbances. If nothing is done, the world will be in chaos... Supana makes a decision and takes action!

Supana summons Houtaro and the others, erases the Chemy Cards so that they cannot be re-sealed again, and takes all the Chemy Cards from Houtaro and the others. However, Kyoka and Lachesis appear and reveal Supana's true intentions in front of Houtaro and the others.

When Houtaro learns the horrifying truth about Supana, he approaches Supana with fury. "Why are you always like this?" Houtaro and Supana finally clash!

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!?

Gotchard defeats the Malgam, who threatens the people, but the people of the city still fiercely condemn Chemies and the alchemists. A world where people and Chemies can live together.... Houtaro has no end to his worries.

Supana has lost his driver, and Gigist calls on him to fight with him. Supana refuses, and fights as Valvarad, but is engulfed by the black flames that Gigist unleashes. Supana foresees his own demise... but then!?

Glion, transformed into Kamen Rider Eld by the power of the Philosopher's Stone, summons an army of Dreatroopers. The city and its people are transformed into gold, and El Dorado is steadily approaching completion.

Houtaro tells his mother, Tamami, that as a Kamen Rider he will create a future where humans and Chemies can live together, and that he doesn't want to run away from his Gotcha! He then joins Rinne, Supana, and the other Chemies in a final battle to defeat Glion!