Man with a strong magic power is called as “Gate” and Phantoms seek and attack them. Kamen Rider Wizard / Haruto Souma, himself was also a “Gate”, fights for a hope of people with a power of Phantoms within.
When strange magical creatures including something resembling the Minotaur begin to attack in Toriizaka, they are all confronted by a man with a strange ring and belt calling himself "Wizard".
Shunpei Nara decides to go on live television to show off his burgeoning magical powers while Haruto tries to deal with both the young man and Hellhound's attempts to attack him now that it is clear Shunpei is a Gate.
Shunpei, the donut shop worker, and Wajima all fall for a woman selling power stones, but she sticks close to Haruto, particularly when a Phantom appears to be chasing after her.
After a mysterious white Garuda delivers a new Magic Ring and stone to Omokagedo, Medusa sends out Ghouls to attack a young boy who is suspected of being a Gate as Haruto finds himself facing Phoenix.
After finding out that Hiroki is the son of his old friend Mikiko, Haruto suggests that he watches over him until the Phantom case is solved. However, Phoenix attacks Mikiko instead of bringing Hiroki into despair and when Haruto realises this, he searches for his father.
The National Security Agency's Section Zero obtains a green Magic Stone, and so Kizaki abducts Wajima so he can commission his own Wizard Ring. At that time, a Phantom arrives to create a new Phantom from a child traveling from Akita to Tokyo, leaving Haruto alone on his mission.
After receiving a new Magic Stone from Kizaki, Shunpei believes that Haruto's abilities are getting better enough for him to start teaching him magic. Meanwhile, a high school student named Tetsuya begins an apprenticeship at a wagashi store and is targeted by the Phantoms.
Around Christmas time, Misa locates a new Gate in the form of a young man with a Yankee fashion sense named Tatsuro, and Haruto must get to the bottom of what his hopes are in order to protect him from becoming a Phantom.
Haruto's and Kosuke's differing ways of handling things, from how to approach the issue on Phantoms to even eating doughnuts, causes a rift between the two magicians.
The three-way battle between Kamen Rider Wizard, Kamen Rider Beast, and the Phantom Hydra continues, with Oikawa's livelihood at stake as he is on the verge of becoming a Phantom. To try to get Kosuke to change his mind, Shunpei and Rinko tell him what really happens to Gates when they fall into despair.
While Haruto tries to help Shiho, a housewife whose life is falling apart around her after being attacked by Ghouls and the new Phantom, Rinko tries to discover the identity of a young man who got into a drunken fight, without knowing that he is the Phantom Phoenix.
When Rinko disappears and all that's found is her bloodied ID, Haruto seeks out her attacker, unaware that Yugo has disobeyed Wiseman and acted on his own volition, with Rinko in the way of his goals.
With Rinko's life on the line, Haruto readies himself for a battle with Phoenix who has become more powerful, despite Kosuke's intention to take Phoenix's magical power for himself.
Gremlin and Weretiger keep Shunpei hostage and offer to free him in exchange for Toshie. Meanwhile, Kosuke has a crisis over his choice to become the Ancient Magician, as it has brought danger to his loved ones. Toshie, however, is willing to give up her life to free Shunpei...
Kosuke discovers Medusa's true identity as the school-aged girl Misa and attacks her, only for Rinko to arrest him. Going on the magician's hunch that she's after another schoolgirl as a Gate, Haruto and Shunpei attend the school to try to thwart Medusa's plans.
When it is discovered that Mayu is the twin sister of Misa, the girl who has become Medusa, Mayu makes it her mission to seek out the one part of her sister that is still alive within Medusa, even though Haruto believes it is better to save Takako first.
Kosuke is meeting an archeologist to get the new Beast Color and a gun-like weapon. However, the BeastDriver is suddenly stolen. To make things worse, Gremlin and a new Phantom appear to defeat the magicians.
Gremlin unleashes a dangerous Phantom who assumes form of a man called Naitō. But unlike the Phantoms Haruto and Kosuke had faced before, Naitō is attacking humans without discrimination.
Nitoh's high school friend Tsuchiya arrives in town, having discovered a job offer that will pay ¥1 million for a day's work. Nitoh joins him on the interview, but Haruto and Koyomi suspect something is off.
Haruto and Nitoh must race to Tokyo to save Tsuchiya, who has won a shopping spree at a mall, as well as 5 other contestants, from falling victim to the Phantom Bogy.
While Haruto and Rinko send by Kizaki to investigate Gremlin's human identity as Sora, Nitoh and Shunpei help save a young woman attacked as a possible Gate, only to discover that she is their favorite fashion model Chiaki. Meanwhile, Gremlin is acting stranger than usual...
With Chiaki revealed to be the Gate sought out by Argus, Omokagedō group tries to figure out what her despair may arise from, with Nitoh believing it may be her loss of popularity. Elsewhere, Haruto has met with Sora, the Gremlin Phantom, and upon realizing that not is all it seems, asks Rinko and Section 0 to investigate, and they discover what exactly happened to Sora Takigawa, as Haruto suspects the Phantom still has his human mind.
With Sora's words in mind, Haruto meet Wiseman to get answers. Meanwhile, Rinko investigates an arson case with Shunpei, only to discover that a man with a caged myna bird may be a Gate.
The group must protect Nemoto from both the Phantom Raum and the police who want to question him on an arson case. However, can they clear Rinko's name before it's too late?
When Haruto goes to save a soccer player from a Phantom, the man recognizes him, and Haruto's former dreams of being a professional soccer player are revealed. Elsewhere, a well-dressed man enters the Omokagedō, although his reasons are not clear.
With Kazuya in the hospital, Haruto must find a way to defeat the Phantom Bahamut, even though the Phantom is much too powerful for him as Kamen Rider Wizard. Meanwhile, the mysterious Fueki commissions a Wizard Ring from Wajima.
While Rinko tries to investigate Fueki, Nitoh starts to teach a boy named Yuzuru to ride a bicycle after he watches Kamen Rider Beast battle a Phantom and his Ghouls with a mountain bike.
With Mayu now as Kamen Rider Mage, she focuses her attention on her former sister Medusa, with Haruto asking her what her true goals are now that she is a witch. Meanwhile, Sylphi continues its attack on Yuzuru, just as White Wizard gains interest in him as well.
Haruto is alarmed to find Kizaki has disappeared after he has been asked to search for Fueki, who kidnapped Yuzuru to seek out another person worthy of becoming a magician. After Kamen Rider Wizard saves Saionji, a novelist, Saionji reveals he is looking for a young woman to give him the inspiration to write again.
Saionji reveals it is Koyomi who he has been looking for all this time, saying he met her once 10 years ago. Meanwhile, Sora warns Nitoh about White Wizard, and he prepares to face him in battle as Kamen Rider Beast and Beast Hyper.
Haruto discovers that Koyomi is the daughter of Fueki, but he keeps this to himself. Meanwhile, elementary school teacher Yoshikazu Kumagai, who comes to the Omokagedō to purchase an antique toy plane for his late son, is discovered to be a Gate when he is attacked by the Phantom Siren.
Haruto must split his attention on saving Kumagai from Siren while they try to find a toy for his son and revealing what he knows to Koyomi about her past. Meanwhile, a red crack appears on Koyomi's hand. What does this mean? Medusa and Mayu face each other again.
Mayu approaches White Wizard asking to become stronger so she may defeat Medusa. Haruto and Nitoh have trouble battling a fast moving Phantom. Sora approaches Haruto at Hungry, inquiring as to whether or not he has found out about Koyomi's past.
Even though Haruto reveals that Koyomi is Fueki's daughter, the group keeps their mission to save Yamamoto from Arachne, particularly when his pregnant wife Aya goes missing.
With the knowledge that Fueki is not only White Wizard, Koyomi's father, and the Phantoms' leader Wiseman, Haruto, Kosuke, and Mayu work together to try to discover his true plans.
With Yamamoto and Yuzuru both Kamen Rider Mages under White Wizard's thrall, Haruto and Koyomi are kidnapped to begin the new Sabbath. After Kosuke is approached by Beast Chimera in his dreams, he goes to assist Rinko and Shunpei to help save Haruto and Koyomi.
Haruto finds he must battle White Wizard on his own for Koyomi's sake after Kosuke uses the last of his mana to disrupt the Sabbath. Elsewhere, Yuzuru and Yamamoto come to their senses and plan to fight alongside Mayu and Haruto for Kosuke.
With Gremlin in possession of the Philosopher's Stone, Koyomi dies. However, Fueki says that the light in Haruto's heart is the true Philosopher's Stone. Meanwhile, Gremlin, now evolved, goes on a rampage, and Kosuke cannot battle to save anyone or even himself from the monstrous Phantom.
After Gremlin's defeat, Haruto is lost in the World of Kaijin, a parallel world where it is inhabited by monsters created by an entity called Amadum who wants to steal the powers of the Kamen Riders for himself. Using the Legend Rider Rings, he will summon 13 Heisei Kamen Riders.
