Takeru Tenkuji strives to be a Ghost Hunter just like his late father, Ryu Tenkuji. On his 18th birthday, he receives a Ghost Eyecon as a present from his late father's spirit. However, a mysterious monster appears, demanding that Takeru hand the Eyecon over. Takeru boldly confronts the monster, but...

Takeru has been revived from the dead and has obtained the power to transform into Kamen Rider Ghost. However, he now has only 99 days to obtain the Eyecons of 15 heroes. Akari, who can't cope with the lack of any logical and scientific sense this situation makes, is called by her professor to where another strange event has occurred. Meanwhile, Onari, knowing that the Gamma are targeting the hero Eyecons, instructs Takeru to go wherever strange events happen and sends him to the same place. Takeru finds out from the Hermit that the next hero to appear is Thomas Edison. However, he has no clue how to summon him. Meanwhile, the mysterious man in black is meeting with an inventor. What is his objective now?!

Sennin gives Takeru three hints: "England, woods, and gentleman thief". After hearing this, Takeru realizes that the next Eyecon is Robin Hood's. As if it were fate, a modern day thief has been going around the city robbing the rich and giving money to the poor while calling himself Little John. Takeru decides to track down this Little John but...

Takeru, who has obtained his third Eyecon, is told by Sennin that the fourth one, Oda Nobunaga, is not going to be easy to obtain. A new client, Kuroda, has come to the Mysterious Phenomenon Institute requesting their assistance as their president of the Sengoku Corporation has suddenly become cold and tyrannical and things have been seen floating around at the company’s headquarters. Could this be the work of a Gamma? Takeru starts investigating. Clues include the letter from a famous Japanese general and the suspicious behaviour of Sakuma, one of Kuroda’s secretary.

The apparent sounds of a machine gun in a supposedly abandoned school, about to be remodeled, catch the attention of Takeru and he decides to investigate. Takeru rushes to the elementary school to find the Gamma. As Takeru fights against the Gamma, the Rider that stole the Nobunaga Eyecon appears again and attacks Ghost. As this Kamen Rider attacks Takeru, he allows the Gamma to get away!

The fear and insecurity of his last two defeats against Specter have made Takeru unable to become visible. An uneasy Akari begins to fear that Takeru will no longer be visible to her, even with the Shiranui powder. A new client seeks the help of the Mysterious Phenomena Researchers. Sound has disappeared around Kosuke Kimijima, a young prodigy composer. It is like Beethoven... Takeru, Akari and Onari pay a visit. While unable to hear, Kimijima starts composing non-stop and Takeru is unable to warn him that he is in danger. A new Gamma appears and Takeru transforms into Ghost. However, Specter appears again to get in his way.

The next hero seems to be Billy the Kid. Takeru immediately gets Sennin's clue and at the same time, a new client comes to the Laboratory saying that something is wrong with their best friend. At the same time, Narita and Shibuya bring information of a sighting of the Mysterious Man. Akari and Onari follow the clue to the Mysterious Man and see him talking to Specter. The man, whose name is Saionji, talks about "what happened 10 years ago..." All the inhabitants of the apartment building the friend lives in seem to be acting strangely as well. Takeru investigates and a Gamma appears. Takeru transforms into Ghost and fights but Specter appears. Takeru, who now has lost all fear, confronts Specter as well.

Ghost was able to defeat the giant Gamma with the Iguana Ghostriker and rescue Akari and Onari from the Gamma Commandos. Specter confronts Saionji, the mysterious man, who talks to him about what happened 10 years ago. The people from the apartment complex were being drawn to a monolith very similar to the one at Tenku Temple. It seems that the Gamma, Specter, Alain and Saionji all have their respective agendas.

Specter turns out to be Makoto, Takeru's childhood friend that had gone missing 10 years ago. What "hell" is Makoto talking about? What was his father researching? Takeru cannot hide his uneasiness as Sennin, as usual, doesn’t provide any answers. Reports surface about strange events ocurring in the laboratory of Professor Igarashi, an authority in physics who also went missing 10 years ago. Igarashi was an acquaintance of Ryu, Takeru's father. There may be some information about Makoto... Among the things, he finds a photograph of them with Saionji. A new character appears before Alain and Saionji takes the next step in his plan.

Takeru has decided to gather the 15 Eyecons not to recover his life but to revive Kanon, Makoto's sister. Akari and Onari are in total disagreement. Takeru loses his words at the feelings of his friends. Makoto appears before Takeru and Akari and transforms into Specter, intent on stealing Takeru's Eyecons. However, Takeru tells him of his intentions to revive Kanon. Makoto lowers his weapon, taken aback by the similarity between Takeru's plead and that of his father, Ryu. Now that the Benkei Eyecon has appeared, Saionji prepares to steal the Eyecons from both Makoto and Takeru. At the same time, the newly arrived Jabel seems to have an additional agenda which Alain seems not to know.

With all 15 Eyecons gathered, Saionji barges his way into Daitenku Temple to the Monolith to demand the ability to take over the world. However, Takeru is taken into a giant mandala called the Great Eye that has appeared in the sky and is asked one question by a disembodied voice: "What is your wish?"

Takeru's wish to bring Makoto's sister Kanon back starts their search for the Eyecons all over again, but without the Gamma to point the way where they have scattered, Akari and Onari are worried that they are too late to bring Takeru back to life. The return of the Gamma Superior means they are on the right track, but something happens to Takeru after he transforms into Kamen Rider Ghost, again.

Thanks to his father's soul, Takeru is still free to collect the 15 Ghost Eyecons once more, and by doing so, he can also bring his father back. But first, he encounters the soul of Sakamoto Ryōma, who poses a challenge for Takeru before he willingly joins him, which he describes as a "Satchō Alliance". Along the way, Takeru must deal with a new Gamma, as well as the return of the Katana Gamma.

Nagamasa, an artificial satellite developer, wanted to follow in the footsteps of his father Satsunoshin and his brother Yoshiyuki, both pioneers of the trade. He dreamt about working together with them to create an artificial satellite. Unfortunately, when they were about to build one, Yoshiyuki passed away in a freak accident causing Satsunoshin to retire out of grief. In order to fulfill Nagamasa’s dream, Takeru tries to convince Satsunoshin to continue building the satellite. However, after the Planet Gamma's attack, Takeru tries to make it his priority, but Onari persuades him to focus on helping Nagamasa resolve things with his father Sachinoshin first. The split between father and son has something to do with the past, and Takeru must figure out what that event was to resolve their differences before the Planet Gamma attacks, again. ​

The Fukami siblings, Makoto and Kanon, are approached by Alain and Jabel. Makoto attempts to fight Jabel but is overwhelmed, which results in Kanon being kidnapped. Knowing that he can't beat Jabel as he is, Makoto tries to use the Eyecon of the "Escape King", Houdini, even though it never let him use its power before.

Takeru decides that he must follow in his father's footsteps and figure out a way to stop the Gamma by preventing them from ever entering the human world. However, the sudden appearance of several Gamma Commandos leads them to put these plans on hold, particularly when Takeru and Makoto discover that they are being led by a new enemy.

Alain, now able to transform into Kamen Rider Necrom, makes easy work of fighting Ghost and Specter. However, for Takeru, it was Alain's words, not the defeat, that bothered him the most. Strange incidents of young women being attacked within a thick mist have started to happen. A woman able to make predictions about the next attacks, Miwako, appears. Onari firmly believes her while Akari denies everything. All the same, they go to the predicted area. The prediction is fulfilled and a Gamma attacking women appears. Takeru is busy looking for the Newton Eyecon so Onari decides to confront the Gamma with his staff...

When the spirit of Himiko isn't the cause of the strange happenings in the city, the Himiko Eyecon leads Takeru to the Gamma World for a revelation. With Makoto also out of action during the continued attacks on young women, Akari and Onari step forward to try to discover the reason for the attacks, but Akari must first improve the Shiranui formulation.

Alain has turned Makoto into Necrom Specter and now has full control of him, calling him the "perfect friend". Takeru immediately denies this and promises to get Makoto back. Igor, using a Gamma's special powers, has infiltrated a company building. Meanwhile, numerous objects have become drawings in the city. It seems that a new Gamma has appeared. Takeru locates it, transforms into Ghost, and attacks but the Gamma does something nobody could expect... Kanon, wanting to save her brother, searches for Alain by herself.

Takeru tries to teach the Gazai Gamma the meaning of friendship, but must also deal with both Igor and Necrom Specter seeking to destroy the "incomplete" Gamma.

Takeru discovers that Makoto's real body still exists in the Gamma's world, and once that disappears, Makoto will as well. To save Makoto, Takeru enlists the help of Akari who tries to use the Gazai Gamma to figure out a way to save Makoto, but Makoto has already gone off on his own to settle matters his own way. ​

Igor, while tending to his progressing plan, orders the Katchu Gamma to destroy the traitor Gazai Gamma. Meanwhile, having sent Takeru to the Gamma world, Akari and Onari decide to not waste time and resume investigating Deep Connect. However, the Katchu Gamma appears. Takeru, without the support of the heroic Eyecons, starts looking for Makoto. Can Makoto settle things and return? Adel's scheme is about to take action and will change the world completely.

Takeru is horrified at the things he witnessed in the Gamma World, but now with all 15 Eyecons gathered once more with Alain now an ally, he wonders what to do for the future. Their plans are waylaid when Adel sends Jabel to the human world once more to kill Alain.

Akari and the others cannot believe that Makoto, who saved Alain from harm, was only an Eyecon. Takeru, now knowing that Makoto’s body is in the Gamma world, intends to go but the others stop him. Kanon offers Alain’s help but Takeru does not trust him. After witnessing this, Kanon goes by herself to convince Alain. Sightings of a Mouse Monster have been reported. It seems to be different than a Gamma. On top of that, Goemon’s ghost has possessed Onari. Alain is still the target of assassins and he still cannot get used to a flesh body and the fear of death. The appearance of a red warrior will further complicate things.

Takeru is now more resolute in bringing Makoto's body back from the Gamma world and Alain seems to have agreed to help. However, Akari is the one to stop them, stating that "It is not time yet." Akari senses that something is going through Alain's mind and is determined to find out more. Igor issues new orders to Bills and the Hikoki Gamma. Alain, irritated at the way Akari is seeing through him, goes to Fumi's takoyaki stall and Kanon is there. Suddenly, she falls unconscious. When Alain looks up, the sky is red.