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.

In spite of Takeru defeating the Hikoki Gamma, the red sky continues expanding. Weakened after his battle with Jabel, Alain is suffering the same effects as Kanon from the red sky. Thanks to Akari, things are not going as he intends them to. Alain finds Akari concentrated on her work and approaches silently... While Kanon's condition worsens, Takeru, along with Narita, Shibuya and Onari, go around the city looking for the origin of the red sky. Without any concrete pattern or direction, the group is left in confusion.

Takeru and Alain have returned to the Gamma World. The former returns to save Makoto while the latter is set on finding answers. Takeru, under the impression that they both had the same objective in mind, loses sight of Alain. What are his true intentions? Meanwhile, Akari, Onari, and Kanon can’t do anything but wait. Akari continues trying to break the code of the Monolith while Onari teaches Cubi more about humans. Igor, on his side, continues with his plan. Adel has witnessed the birth of a new threat from the Praying Room...

After witnessing the murder of his father Adonis by his older brother Adel, Alain is unable to move and cannot overcome the situation and feelings it caused. Makoto has obtained a mysterious new Eyecon and goes in search of Takeru, who did not return after his encounter with the Gammaizers. In the human world, Cubi is in a slump. While trying to clear his head, he is confronted by the Onpu Gamma. Akari, Onari, and even Igor are added into the mix. Will Onari and Akari be able to overcome this pinch?

Yuki visits the Paranormal Events Laboratory claiming that she saw her supposedly dead father entering the Deep Connect HQ building. The Houdini Eyecon, for some reason, decides to possess her. Takeru heads to Deep Connect to find out the truth. Having lost his father, Alain is at loss of purpose in his life. Fumi approaches him and acts kindly by giving him new clothes. Makoto appears before him, asking for his help in investigating Yuki’s incident but...

Alain had brought a drawing set for Fumi but her Takoyaki stand is full of people looking worried while an ambulance is seen rushing away. Alain cannot believe what he hears once he asks what happened, his hope fading away yet again... Yuki has infiltrated Deep Connect and it is none other than CEO Steve Bills who finds her, but offers her his help. Takeru and the others come aftewards and, while not fully trusting Bills, they follow him. Yuki finally reaches where her father is but a terrible truth awaits.

Alain has taken a big step by deciding to live as a human with Fumi's memory in his heart. He asks Takeru and Makoto for help. After many difficulties, their objective has unified and they can now fully join forces. Alain proposes destroying the gates that connect this world to the Gamma world. Still at doubt about the recent insight into people's memories he's been having, Takeru agrees to assist Alain. In the Gamma world, Edith questions Adel: "What do you wish for?" Adel laughs this question off and uses his newfound power. As a consequence, many adults have become children around the city, Shibuya’s mother being one of them. The Daitenku Temple is filled with children and a familiar face makes an appearance.

Igarashi has called Takeru into the memories of past times. He finds out a truth that has been hidden for 10 years. The wishes and feelings of his father, Igarashi, Saionji and the Hermit resonate inside him. What could be beyond these strange changes Takeru is experiencing?! Meanwhile, Shibuya is looking for his mother, who has escaped yet again. More and more adults are being turned into children. Society itself may spiral out of control. Everyone is running against the clock to solve the mysterious phenomenon the new Gammaizer has set in motion.

Gammaizer Gravity begins to attack alongside Gammaizer Fire, causing significant damage. Alain attempts to defeat Gammazier Fire with a kamikaze-like ability of the Necrom system to protect Takeru, but is knocked out of his transformation at the last moment. The unexpected happens when Gammaizer Gravity both defeats Ghost, and destroys his Ore Eyecon, causing him to vanish. Takeru's absence saddens his friends and allies and while they discuss how to revive him, the Gammaizers reappear. Akari opens a portal to send them to another world, but the plan fails when they managed to escape and soundly defeat the other riders. Akari and the others vow to not give up, and their resolve and emotions not only revive Takeru, but grant him the Mugen Eyecon. Takeru returns with new strength and destroys Gammaizers Gravity and Fire. Is this new power only a temporary halt to Takeru's death, and can it permanently destroy the Gammaizers?

Thanks to Takeru's friends being able to revive him through the destroyed Ore Ghost Eyecon, he was able to defeat the immortal existence of the Gammaizer thanks to a new form made of light! Yurusen, who helped to revive Takeru, still remains as a ghost. And Sennin is beginning to talk about Takeru's own existence. The fact does not escape Sennin, as he himself doesn't know what state he is in now. Although there are less days now until his death, he seems to have revived completely. Meanwhile, Akari's teacher won't wake up from the Dream World, as they discover that Igor is eventually behind all this. Adel sends in a new Gammaizer, but still wary of Takeru's new form. As the battle in the Dream World begins to heat up, Takeru's rider of light appears once again...

The Dream World Takeru and the others were investigating was another one of Igor's schemes. Jiro, brother of Akari's professor, Yuichi Katagiri, insists that he won't leave the Dream World. The brothers' squabble catches the attention of the Grimm Eyecon and the Brothers Grimm themselves start having a discussion about fun. Due to this, Grateful Damashi can no longer be maintained and the Eyecon is stolen. A new Gammaizer has appeared as well. In the meantime, Makoto and Alain, tasked with protecting Takeru’s body, confront a Gammaizer themselves in the real world.

Igor changes his strategy after Ghost Mugen Damashii defeats another Gammaizer. Takeru finally knows the true meaning of fun thanks to the Brothers Grimm. Also, a new Gammaizer that controls wind appears before Takeru. Deep Specter and Necrom are being attacked on all sides. Alain cannot stand the idea that he might not be able to protect the treasures of this world. Meanwhile, Bills attempts to put his own plan into action by attempting in on an idol, to which Akari decides to replace. Apparently, this plan is connected to his goals from his own childhood. In order to re-inspire belief, Sanzo sends Alain to a training field in another world. But Akari and Onari also seem to be targeted by Igor's plans as well...

After confirming that she hears other people's thoughts, Takeru visits Honami's group members once again in order to help. Honami hears their thoughts, still saying only bad things about her. On top of that, Igor has set a Gamma on her due to her power and she feels now, more than ever, like quitting for good. Alain, on his part, is on the verge of defeat as well in the trial world he was sent to by Sanzo. Akari, who for some reason passed the audition for harp+y 4, is now faced with Honami's pressure but she decides to give her best. Meanwhile, Makoto encounters his other "self", the one Kanon told him about. In the Gamma world, the Gammaizers talk to Adel and tell him it is time to obtain new power.

Jabel become frustrated due to fight always lose. Jabel in vented anger by damaging the forest. Takeru and his friends tried to make Jabel quieter. Onari Takeru who asked that she only entertaining Jabel. Adel and Gammaizers appear together Takeru challenged to a fight. All the heroes spend Takeru for help. But all the heroes it easily defeated by Gammaizers. More striking the Gammaizers joined to the body of Adel. Adel became very strong. Makoto meet again with Copy Makoto. The effects of the defeat Copy Makoto into the wound for the Makoto original. Takeru tried to rebuild the trust of the heroes who lost a fight. Confidence heroes to Takeru grew after the fight Gyro together.

The meeting between Adel, Alia, and Igor commence. At the beginning of the debate Igor gets a blow from Alia. While Adel "defeats" Alia when she changes into Dark Necrom, his strength is still not comparable with the Gammaizers. Takeru encounters a debate in the house of a Father and a daughter. After arguing they were attacked by a Gammaizer. The Gammaizer appeared to look weak compared to the previous but the soul of the father and daughter swapped bodies. Billy the Kid appears and enters the body of Kanon. Takeru works to help resolve problems between the father and daughter. The father turned out to have a new relationship with the fugitive known by Mayu the daughter. While the Dad was in the Gammaizer's body, Mayu in her Dad's body, and the Gammaizer in Mayu's body, can Takeru and the gang solve this mystery and find out what he's after?

In an effort to help Mayu and her Father - Shinichiro - Takeru and the others help Mayu to solve the source of a leak in her Father's workplace - which her Father's partner suspects is her Shinichiro...

Takeru only has 19 days left. Feeling uneasy at the fact that he is apparently losing his humanity, he talks to Akari. She assures him that they will do whatever they can to help him revive. However, Takeru is troubled by his powerlessness. He calls the Hermit but Akari is infuriated at the old man's response. Beethoven possesses Akari in her rage, greatly increasing it and causing a ruckus at the Tenkuji Temple. Everyone tries to think of a solution. Meanwhile, in the Gamma world, Edith has decided to put a stop to Adel. He obtains an Eyecon when Adel tries to connect with the Great Eye, however he only managed to break the connection and send Adel into the human world. Adel and Edith fight. Takeru and the others come to his aid. Edith and Takeru's encounter will lead to the truth about the Gamma World.

Edith makes an attempt to stop Adel but had it not been for Takeru's intervention, he would have perished. At the Tenkuji Temple, Edith finally explains the workings of the Gamma world, whose origin is something completely unexpected for the rest. Edith was behind the creation of the Eyecons and the Gammaizers. Adel makes an appearance again and it is now Makoto who gives his all facing him. However, he is defeated and suffers major injuries. Adel tries to connect to the Great Eye again and he is rejected. Adel's anger now fully directed towards Takeru, he makes a third appearance in the human world and this time Alain faces him.

The people at Tenkuji Temple have become united once again and are now joined by the Hermit/Edith. They pay a visit to Ryu's grave where Takeru vows that he will come back to life. Meanwhile, after losing to Takeru and destroying his Eyecon by himself, Adel returns to his real body and enters a dormant state. A new client visits the temple, saying that their child is behaving strangely. He is writing long, complicated mathematical equations and singing strange songs. Takeru and Onari go investigate but find something unexpected. Igor's Demia plan is about to be set into motion and a countdown begins. Adel connects with the power source.

Adel's plan is to use Demia to make the human world the same as the Gamma world. Takeru decides to start by destroying the Demia servers. Hiroki has had his soul and body separated. Takeru enters the memories of those connected to Demia. He transforms into Ghost Beethoven Damashii and uses music to help the people recover their memories but...

Adel has connected to the Demia network and taken control of everyone with the intent of becoming a new world himself. In order to stop this, Takeru, Makoto, and Alain transform and face all the revived Gammaizers. In that moment, Takeru taps into Adel's childhood memories. What he sees surprises him... Takeru believes he can stop Adel's rampage by connecting with him. He tries but Adel responds by ordering the Gammaizers to eliminate them all.

Everyone vows to do what they can while Takeru is invisible. Meanwhile, the Gammaizer want to evolve. They order Copy Makoto to study how humans convert feelings into power because Takeru is the key to everything. Takeru watches people get connected to the Demia network when suddenly he gets a headache from all the voices.

After evading its attacks, Ghost Mugen Damashii is able to connect with the Perfect Gammaizer. Takeru witnesses Adel's sad memories of losing his mother. Adel, on his part, connects with Takeru's sad memories of the loss of his father but the words he gives Takeru are completely unexpected… "I killed your father." Adel is Ryu's murderer?! Takeru becomes unable to hold back his rage.

Edith, as Kamen Rider Dark Ghost, welcomes Takeru, Makoto, Akari, Kanon, and Onari to the Gamma World and brings them to Adel but they are stopped by Igor and other Gamma. Igor approaches Akari and she decides to slap him repeatedly until he snaps out of it.

Takeru is on his last day of life as the Ganmaizers revive once again and assimilate Adel's body in order to create an entity completely fused with the Great Eye! The Ganmaizers have decided that humanity deserves to be eradicated, due to their inconclusive emotions and systems of logic and reasoning. Takeru is forced to watch them destroy large sections of the city! Makoto and Alain fail to stop them as their power is greater than normal! All hope lies in Takeru who tries to deal a final blow to the Ganmaizers but to no avail! They watch as they begin to disappear large amounts of people from the city...

Takeru and the others go to Ryu's tomb to let him know that Takeru was able to revive. The Gammaizer menace is no more and everything has gone back to normal. Takeru has returned to school and is being helped by Akari to catch up with his studies. Alain looks up to the blue sky and makes a decision. Makoto, who with Kanon has seen off Takeru, lets his sister know of a decision of his own. A strange young boy holding a mysterious artifact appears and says: "The one with the power to change the world." What is the meaning of these words? The boy is attacked by the black Kamen Rider that appeared before.