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 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 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...!?

In order to save the drama club, Houtaro and his friends decide to help put on a performance of "Romeo and Juliet". Mikuriya, the head of the club, selects Houtaro to play Romeo, while Seina, a transfer student and childhood friend of Houtaro, runs for the role of Juliet, while Rinne is put off by the fact that she is not a member of the club.

Rinne is bothered by Houtaro and Seina's sudden closeness. Atropos appears, sees through Rinne's emotional turmoil, and unleashes a Malgam. Rinne desperately defends Seina who is nearby...!

"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...!

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. Then, suddenly something unusual happens and a new enemy appears to attack Houtaro and the others...!?

The Dark King Gigist appeared at the Union headquarters. Supana, angered by Gigist's defeat of one of the Union leaders, transforms into Kamen Rider Valvarad. He boldly attacks Gigist, but...

Gigist appeared in front of Houtaro, took away Skebows' card, and turned it into a Malgam. Houtaro transforms into Gotchard and challenges the Malgam to save Skebows, but he feels something strange in the battle...!?

Houtaro and others show Kyoka the completely white Skebows. They want to somehow regenerate Skebows! Houtaro and the others look at it as if praying, and Kyoka...!?

Hopper1 sets off alone on a journey to find "something" to cheer up Houtaro. Meanwhile, Gigist has taken Antrooper from Houtaro and turned it into a Malgam. The Malgam attacks people, and Houtaro and the others...!?

Houtaro, who was spirited away from Rinne and the others by a giant egg, finds himself in a black space with a floating blue egg. "What is this place? Who are you?" Houtaro asks the egg.

Gigist stands before Supana, who was on his way to rescue Houtaro. Supana transforms into Kamen Rider Valvarad, only for Gigist to unleash the mighty Malgam, which he had created by rallying his Chemies, on Kamen Rider Valvarad!

Renge proposes a competition to retrieve the two remaining Chemies, with Nijigon at stake. Despite a stunned Houtaro, Rinne, Sabimaru, and even Nijigon get involved...!

Gigist appears before Houtaro. Gigist tries to dye the Chemies in darkness, but Houtaro uses the power of Nijigon to prevent him from doing so. He transforms into Rainbow Gotchard and clashes with Gigist!

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!

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!