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.

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.

Houtarou continues his quest to befriend all the Chemies as he meets a Chemy known as Apparebushido, and is given his card by Minato.

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.

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.

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.

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.

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.

Hijiri, whom Kajiki is in love with, has a boyfriend. Although Kajiki is depressed, he learnt that Hijiri's boyfriend is most likely the remaining suspect who made his escape after Clotho attacked the police van.

Clotho captures a new Chemy, UFO-X, in Kyoto. It seems that it has something to do with the mysterious driver that the Three Dark Sisters are plotting - Meanwhile, Houtarou and his friends continue to work hard to recover Chemies.

The spy for the Three Dark Sisters turned out to be Shiori Harima, an investigator from the Alchemy Union. Houtarou lashes out in anger at Shiori, who attacks the Chemy, but is tormented by her use of forbidden alchemy.

Houtarou and his friends find a possibility to rescue Sabimaru by befriending UFO-X. However, the Three Dark Sisters and Sabimaru with the Dreadriver appear before them.

Houtaro is asked by Rinne, who has a thoughtful look on her face, to confide in him about a certain problem of hers. Just what exactly is on her mind? Then the two are dispatched to the appearance of a new Level 10, X-Rex.

The raw power of Super Gotchard overwhelms Dread and gains an upper-hand, but Dread is capable of executing counterattacks, resulting in a back-and-forth battle. Meanwhile, Lachesis approaches the daughter-father duo Sawa and Manabe.

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 the new year begins, while Houtarou is serving New Year 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.

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.

Houtaro and his friends are in high spirit 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.

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..."

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.

Renge has fallen under the spell of Zukyumpire. Zukyumpire attracts many men and women, but when Houtaro and his friends investigate, they find that there is a danger to Renge and the others...!?

Houtaro and Rinne try to stop Zukyumpire, who steals energy from people. Then, Renge and others bring one of the Zukyumpire worshipers, Yua, to the scene.

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.

Houtarou has transformed into Iron Gotchard. However, the impact on his body is immeasurable, and Rinne and her friends are worried about Houtarou's health. Meanwhile, it was Fuga Kudo who appeared. What is Minato's shocking "past" that Fuga talks about? And the other Chemies are still taken by Geryon. Everyone heads out to get it back, but the one who appears to bloc...

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.

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.

Renge, who was visiting her grandmother's village, informs Houtaro and the others that a yokai has appeared and she wants them to come immediately.

The village chief is found in a grisly state, and the villagers assume it is the work of Starshine Hoshino and make a big fuss. They lock Hoshino and his apprentice Kajiki in a warehouse. Kajiki would never attack anyone.

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 Hou...

"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.

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.

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.

Kaguya, who is reunited with Houtaro, comes to Furasu High School and charms the students with his "gorgeousness". Houtaro is taken aback by the notoriety that even a fan club has been formed.

Kaguya transforms into Legend and attacks Houtaro. Houtaro also transforms into Gotchard and fights back, but Kaguya shuts him down and says, "Gorgeous time is over," and leaves him alone.

The Dark King, Gigist, finally makes his move. Gigist finds a mysterious egg inside Houtarou. To get the "egg" he has been looking for, Gigist begins his invasion to Houtarou and his friends!. Then a shocking truth is revealed: what are the "true forms" of Chemy and the others?. This is only the beginning of the worst-case scenario drawn up by the Dark King.

After defeating Skateboard Malgam, Houtarou lose Skebows and is overcome with sadness. Furthermore, a Malgam of Antrooper appears in the city and Rinne fight him for the depressed Houtarou, but if she defeats him, the Antrooper will suffer the same fate...?. Rinne is unsure, so Renge and Sabimaru join in to support him. Meanwhile, seeing the depressed Houtarou , Hoppe...

Having lost Hopper1 and fallen into despair, Houtarou was covered by an egg and disappeared... And then, rain began to fall. What is happening inside the egg? Rinne in despair, believing Houtarou will never return. In the continuous rain, his companions, though worn out, keep waiting. When the rain stops and a rainbow appears, he will surely come back with a powered u...

Finally, a full Gotcha of Chemies!? After Gotcha the phantom rainbow Chemy, "Nijigon", only two Chemies left to complete the collection of 101. Each two groups with their unique strategies aiming to Gotcha "Ojilacanth" and "Pakuraptor". However, The Dark King will not just stand by and watch... A fierce assault against the threat of Nijigon!? When all 101 Chemies are ...

The Dark King was not alone!. The final kings come from the Ouroboros ring. Their names are Germain and Gaelya. "We are originally a trinity," says the regenerating Gigist, while the Dark King, the Transcendent Germain, speaks eloquently. "I love humans...!" "First, for the sake of human happiness, let's go eliminate the most troublesome pest." Fuga Kudo is the target...

As the Dark King Germain continues his fierce attack, Nijigon suddenly disappears. Houtarou and the others desperately search for him. Using clues, they arrive at a place... A dance event venue!? Where did Nijigon disappear to!? Meanwhile, Rinne made a promise with Atropos. Supana receives an invitation from Gigist. Their intentions begin to move, and the story reache...

The 102nd Chemy has appeared!? Based on eyewitness reports of the creature, Houtarou and his team set out to investigate. What they found ahead was Sabimaru's brother, "Kenichi," and the facility where Sabimaru was born and raised, the "Kongo Laboratory." Guided by the director, "Mami Kongo," Supana casts a suspicious eye, sensing something fishy. Is the 102nd Chemy a...

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!?