On his 18th birthday, Takeru Tenkuji receives a gift of a strange item called an Eyecon from his long lost ghost-hunting father Ryu, who left years before to try to see if ghosts actually exist.
In order to revive himself, Takeru must find 15 Hero Eyecons before his 99 days are up. Having already obtained Musashi, he sets out to find the remaining 14 Hero Eyecons.
After hints from Sennin, 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 stealing from the rich and giving to the poor while calling themselves 'Little John'.
Sennin tells Takeru that the next Eyecon is Oda Nobunaga's but it is currently unobtainable. Meanwhile, he is alerted to odd activity at an office building where things are mysteriously floating. Could it be the work of a Gamma?
Takeru, Akari, and Onari investigate a young musician who seems to have all sound around him disappear, but when another Gamma appears, Kamen Rider Ghost and Kamen Rider Specter battle each other once more, all over the spirit of Beethoven.
Sennin informs Takeru that the next hero he should seek out is Billy the Kid, and that it will be near one of his close friends. However, Takeru instead finds Makoto Fukami and he confronts him on what his true intentions are.
Specter confronts Saionji, the mysterious man, who talks to him about what happened 10 years ago. Meanwhile, residents of a nearby apartment complex are being drawn to a monolith similar to the one at Tenku Temple.
Takeru has decided to gather the 15 Eyecons to revive Kanon, Makoto's sister - instead of restoring his own life. Akari and Onari are in total disagreement, arguing that his life is just as important as hers.
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 Gammas to point the way, Akari and Onari are worried that they are too late to bring Takeru back to life.
Thanks to his father's soul, Takeru is still free to collect the 15 Ghost Eyecons once more. But first, he encounters the soul of Sakamoto Ryoma, who poses a challenge for Takeru before he willingly joins him.
Onari persuades Takeru to remain focused on helping Nagamasa resolve things with his father, Sachinoshin. Takeru must figure out how to resolve their differences before the Ganma attack, 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.
Takeru decides that he will follow in his father's footsteps and figure out a way to stop the Ganma. However, the sudden appearance of several Ganma Commandos leads them to put these plans on hold.
Strange incidents of young women being attacked within a thick mist have started to occur. A woman able to make predictions about the next attacks, Miwako, appears.
The Himiko Eyecon leads Takeru to the Ganma 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.
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.
Takeru tries to be friends with the Ganma who likes to paint, before learning that Kanon has been spotted alongside Alain. Worried that she is in danger, Takeru goes over to rescue her, and encounters Necrom Specter.
