Set after the Kamen Riders defeated Kamen Rider Cronus, a new outbreak of Bugster virus occurs one rainy day with a large number of people becoming sick. One girl goes over to try and help a man who had collapsed, only to be hit by a glowing shuriken which then goes into her body and she starts to have symptoms of game disease. Before she passes out, she sees the culprit, a lone armored figure on a lamppost with his arm outstretched. At Machina Vison, the game company's CEO Johnny Maxima is pleased when a mysterious figure named Kagenari reports the progress of the epidemic. He inquires about Kagenari's choice for a "Player", a terminally ill girl named Madoka Hoshi. Kagenari tells him that she will be the perfect choice for their experiment.
At Seito University Hospital, Asuna and Emu are checking up on Madoka. The little girl is sad she is stuck in the hospital getting treatments, as she wants to be at school with her friends and run in an athletic meet. Emu reassures Madoka if she gets her treatments she can go home and be in school again, but doesn't say anything about running. Makoka's mother Akemi tries to calm her down, but Madoka thinks Emu is lying and covers up under her blankets. Mrs. Hoshi thanks Emu and Asuna for visiting them even though he is not her doctor, with Emu simply happy he can provide moral support to Mrs. Hoshi in this difficult time. As the two walk, Asuna asks Emu is Madoka will be alright, with Emu saying Madoka's unique condition makes things a little more complicated. They need to find a way to improve her condition before they can consider surgery. Emu wishes he could see Madoka smile again. Suddenly, screams can be heard from the hospital's waiting room as a figure attacks people and infects them with game disease. Hiiro arrives and sees one of his nurses get hit by a shuriken. Two strange ninja figures appear with an unidentified Kamen Rider walking right behind them. Outside, a trio of the ninja grunts are attacking people with Taiga and Nico doing what they can to get people out of the line of fire before engaging them.
Emu, Asuna, and Hiiro all transform to try and fight off the ninjas in the hospital while Taiga transforms into Kamen Rider Snipe Level 2 to battle the ninjas outside. Kamen Rider Poppy tries her best to fight, but the sheer numbers and strength of her opponents knock her out of her transformation. Soon Hiiro and Taiga are defeated as well, as the enemies begin to multiply and outpace thier attacks. All three of them and Nico are hit with a shuriken and collapse. The Kamen Rider from earlier used his minions to distract and eliminate anyone from interfering while he heads to Madoka's room, knocking out Akemi when she tries to protect her daughter. Emu as Ex-Aid tries to keep the Rider away from Madoka, but he is no match and the Rider uses a Hurricane Critital Strike to blast him away and knock Emu out of his transformation. The Rider deactivates his Gamer Driver, revealing himself to be Kagenari. He enters the room and uses a Bugvisor with a blank Rider Gashat in it to infect Madoka, which causes her to black out. Emu races into the room and tries to help her, but is smacked aside by Kagenari, who then takes his leave having accomplished his mysterious goal.
After the opening title, Asuna is in her Poppy persona and finds herself outside on a school track field during an athletics event with no idea of how she got there. She is even more shocked to find Taiga is the coach, firing a gun at the starting line for the race and Nico is the referee. Madoka is happy and running to her mother saying she is up next in the 50 meter dash, with Hiiro acting very strange, happy, smiling and thinking he is Madoka's father and carrying a camera to film his "daughter's" sporting event and his beautiful "wife". It is revealed that all of them are comatose in the CR and trapped in some strange collective dream. Emu is struggling to deal with the large influx of patients as a large portion of the hospital staff have been infected and are also comatose. Emu scans one of the patients with the Game Scope, but it reveals that while this outbreak matches game disease, there is no Bugster data that it can use to determine the cause.
Back in the "dream", Madoka is racing in the 50m dash while her "dad" is watching, but Hiiro is interrupted by Poppy who wants answers as to what exactly is going on. Hiiro surprisingly doesn't remember who Poppy is and is terrified of her as she gets in his face. Madoka wins the race and Nico congratulates her. Poppy then hears a familiar sound: "GAME CLEAR!" and sees a black Gashatrophy appear above Madoka's head before disappearing again into a digital void.
At Genm Corp. Kuroto confronts Tsukuru Koboshi and accuses him of being behind the new Gashat, as only Tsukuru and himself are the only people capable of making Genm Corp. games. Kiriya on the other hand thinks that he might have some knowledge on what business Masamune was doing at the time he was CEO of Genm Corp. Tsukuru does mention that Masamune tried to engage in a business deal with Johnny Maxima, CEO of rival game company Machina Vision. A Gamer Driver and data on Kamen Rider Chronicle's development process to create a brand new game were Johnny's conditions for working with Masamune but he refused. After the meeting ended, Genm Corp's servers were attacked by hackers and the Gamer Driver schematics were stolen along with the company's Rider Gashat development data. Machina Vision has the resources to create a Gamer Driver and apparently sent their lackey to use it in a field test. Kiriya suspects that all of the people in a coma are probably trapped consciously in the Game World.At Machina Vision, Johnny and Kagenari discuss their plans to move onto the next phase of the experiment using the people they trapped in the Game World.
Back in the game world, Hiiro is ready to have lunch with his "family" by cutting a personal pan pizza. Akemi gives Madoka a slice and she smiles as the pizza is yummy, which causes the Gashatrophy to appear again over her head. Poppy sees this and wonders what it could mean. Madoka becomes sad again and wonders if "he" will be happy now.
Back in the hospital, Emu watches over Madoka and figures out based on the fact that the others are talking in their sleep that they are in a "dream" where they are in Madoka's school during the athletic meet and begins to put the pieces together.
Johnny says that Kagenari is a really sadistic man, using his own daughter as a "player" in his game. Kagenari says that it is all for the support of his vision. Kiriya appears, having eavesdropped in data form to hear their plans. Kiriya asks Johnny if he likes ninjas, which he responds that he does, showing him a fan he bought. But Kiriya is quick to point out that the kanji on the fan spells "spring onion", not "shinobi". Kiriya then asks Kagenari what his intentions are, to which the sinister man replies: a happy ending. Kagenari then uses his Bugvisor to infect Kiriya and Johnny, saying that "Mr. CEO" was going to be his player too. Johnny is unsurprised by this sudden act of treachery as he passes out.
In Genm Corp.'s basement, Kuroto has figured out a way for Emu to enter the Game World that the patients are trapped in. The only way to get to the patients in the Game World without being infected is through a VR system Kuroto developed: Genm VR. He also gives Emu a new Rider Gashat so he can fight as Ex-Aid in the Game world if he needs to: Mighty Creator VRX, a game that can create games from the user's imagination. Emu prepares to go when Kagenari's ninjas storm into Genm Corp to stop them. Emu starts up the VR unit after putting on his Gamer Driver and enters the Game World. He finds himself on the roof of Madoka's school with Kiriya there to greet him.
Kuroto is seemingly escorting Emu to his car to keep him away from the Ninja-Players and drives off, only for the car's tires to be punctured by ninja caltrops and the car crashes. Kuroto gets out of the car and faces the Ninja-Players as well as Kagenari's Ninja Gamer Rider form as Genm Zombie Action Gamer Level X-0, but is unable to keep them all away from the car. One of the Ninja Players tears open the car door, only to find Parado in the backseat, revealing this was all a diversion to keep Kagenari away from Genm Corp. Parado changes into Perfect Knockout Gamer Level 99 to fight, but Kagenari flees using his stage select, letting the Ninja-Players deal with the Riders.
Back in the game world, Kiriya explains to Emu that what Kagenari has done is make a world for his daughter that would be paradise. Kagenari appears in the game world and attacks Emu, who at first tries to fight in his base Rider Form of Action Gamer Level 2. The Ninja-Players succeed in killing Genm, leaving Kuroto down to his last life as he prepares to engage the Ninja Players again. Kagenari is infuriated that Ex-Aid is interfering in his "eternity", but Emu thinks that this is no paradise as people are suffering in the real world and it is his job to save them. He then changes into Creator Gamer form using the Mighty Creator VRX Gashat. Kagenari tries to attack Ex-Aid, but Emu's creativity as a gamer mixed with the Gashat's power allows him to counter any attack and conjure up weapons and shields. He then creates a bridge platform and traps Kagenari on it by erasing both ends of it. He then executes a Mighty Critical Strike, creating a bunch of seeker missiles which barrage Kamen Rider Fuma off the platform and keep hitting him during his fall down to the pavement.
Kagenari tells Emu that it is foolish to try to free the people as there is no escape from this world. Emu says in that case he will just create one, creating a pair of rocket wings to fly and creating a portal back to the real world by circling in the sky and using the Mighty Creator VRX Gashat to draw it. The portal sucks up all the trapped people into it, except Madoka. Emu tries to use his flight powers to reach her, but the portal's suction gets stronger and begins dissolving the Game World. Madoka refuses to leave, saying she wants to be here and she will be okay. Her Gashatrophy appears and all of the Game World environments are erased. Emu is sucked into the portal as his rocket wings rip off, unable to save her. Hiiro briefly retains his "dad" persona, crying out for Madoka as he wakes up. The rest of the Riders wake up in the real world and Kagenari emerges only to be at gunpoint by Para-DX, with the last of the Ninja-Players defeated by Genm.
Emu takes off the Genm VR, wondering why Madoka wanted to stay behind. Madoka is in blank virtual space with the three Gashatrophies she created, which Johnny Maxima absorbs into himself upon entering virtual reality. He congratulates Madoka for doing such a good job, saying that he is the ultimate "last boss" when she asks who he is, Johnny's eyes glow a menacing orange and his body becomes covered in a red and black aura.
All of the Riders confront Kagenari, asking why he created that virtual world. Kagenari wanted to make his daughter happy, to give her eternal life in a virtual world when her mortal life in the real world was nothing but sickness and pain. Emu doesn't buy that and thinks Kagenari just gave up on her in real life when she needed him most. Kagenari explains that he was away at work a lot so Madoka never knew what he looked like and he seems to regret not spending time with her. When her health got worse, he couldn't even save her life. Emu also sees this as an excuse, as long as there is hope for the future, there is always a chance for a better tomorrow. As long as anyone can make people smile, there is a chance to make lives better and save them. Kagenari thinks he is speaking nonsense and pushes him, but Emu says nothing is more important for an adult to protect than a child's life and smile. Johnny Maxima arrives and says that he has "saved" Madoka, congratulating Kagenari for being correct on his theory. Using his daughter's happiness to create mini-games she could clear that could create a new power. With this power now flowing through him, Johnny proclaims that he will end the world as its god, transforming into a red and gold variant of the ultimate Bugster: Gamedeus. The Riders quickly change into their strongest forms to fight Gamedeus, but the god-like Bugster swats them away with a powerful black aura and a gust of wind and knocks Emu, Taiga, Hiiro and Kiriya out of their transformations. Gamedeus attempts to kill them all with a blast of flames, but Kuroto and Parado block the attack, push it back and make a suicide run towards the Bugster. The resulting explosion sends their Gamer Drivers and Gashats flying and land near Emu, with Kuroto and Parado seemingly dead. But it was all for naught, as Gamedeus regenerates due to the fact he had infected enough people to retain a portion of his power. The evil villain spares the remaining Riders before leaving, seeing them no longer as a threat and mocking the deaths of their comrades to "enjoy their game of despair".
The heroes mourn Kuroto and Parado at Seito Hospital, but their moment of melancholy is interrupted by Director Kagami coming in and saying there is an emergency: Madoka's vitals are dropping as activity in her cerebral area is getting worse the longer she is in her coma. If they don't operate on her condition now for her illness immediately, it along with her recent coma could kill her. Hiiro wastes no time in agreeing to do the operation, with Poppy volunteering to be his nurse so she can see Madoka smile again. Emu volunteers to aid in the surgery, which Hiiro agrees to. Taiga tells Nico to go be with Madoka, as he is planning on dealing with Gamedeus by himself. Nico tells him to be careful as Kiriya watches him leave. At Machina Vision, Kagenari seems hesitant to go to the final phase of Johnny Maxima's scheme, but thinks that there is nothing in the real world Madoka will miss.
Emu, Hiiro and Asuna enter the operating room to begin the procedure while Nico waits outside with Madoka's mother to give moral support. Taiga is outside Machina Vision, with Kiriya having followed him. Kiriya thinks it was risky and foolish to go alone just to die, as he will go with him whether he likes it or not. If they die, they die together. Kagenari comes out to face the two, transforming into Fuuma. Kiriya faces Fuuma as Lazer, calling him a lousy father as he could be at the hospital during his daughter's operation to support her. Kagenari is outraged, wondering why they would do such a thing as operate on her. Madoka's condition worsens as her body begins to fade from game disease. In this state, Hiiro cannot operate any further without risking her life. Emu and Asuna realize that Madoka wanted to stay in the Game World because she wanted to make her father happy. Emu activates the Proto Mighty Action X Origin Gashat, promising Madoka that he will bring back her real smile by making her wish come true. The effects of the Level 0 Gashat neutralize her Bugster virus symptoms such that Hiiro can operate on her again.
Kagenari as Fuuma is defeated by Snipe and Lazer's Bang Bang Critical Fire and Shakariki Critical Strike combination attack, but Gamedeus appears and confronts them before they can do anything to Kagenari. Gamedeus hits them both and their with a flurry of attacks and their Rider Gauges reach near their lowest point. Brave Legacy Gamer Level 100 saves the two by absorbing Gamedeus's oncoming flaming swordbeam attack into his sword that would have finished Snipe and Lazer off and uses his RPG-themed abilities to heal his comrades back to full health.
While the three Riders battle Gamedeus, Emu arrives and talks with Kagenari about Madoka, her operation was a success but she is still in a coma due to her consciousness not leaving the virtual world and she could still die. He tells Kagenari that what she needs right now is her father and that all Madoka ever wanted was for her father to be happy again. Kagenari refuses to accept this as she barely knows him. Emu rebuts that Madoka may not know him that well, but she loves her father regardless and was willing to risk her own life to make him happy by making his wish come true. Only Kagenari can give his child the willpower to live again by being there for her. Lazer arrives in bike form to offer to take Kagenari to see his daughter, which Kagenari accepts.
Taiga and Hiiro are blasted away by Gamedeus generating a red energy mist and knocked out of their transformations, too beaten up to even move. Genmdues evolves into his second form again and ejects Parado and Kuroto from his body, revealing the two were alive as Gamedeus was using thier Bugster data to speed up his recovery. Gamedeus creates a large and expanding green Game Area bubble and tries to destroy the city, but Emu transforms into Ex-Aid Muteki Gamer form and engages him. Kagenari arrives at Seito University Hospital and rushes into Madoka's room, holding his daughter's hand with Akemi and calling out to her. Ex-Aid uses his Gashacon Key Slasher in its various modes to whittle down Gamedeus, who then tries to crush Ex-Aid under his own weight. He fails as Emu used the invincibility mode of his Muteki Gashat and is determined to change the fate of Madoka, even as Gamedeus rants that fate is a myth and humans are destined to die. Kagenari apologizes to Madoka for putting her in danger, but is happy that his daughter loved him so much and remembered him. He begins to cry and tells his comatose daughter that what he wants more than anything is for her to live and promises from now on that he will never leave her side when she needs him. Madoka hears her father and starts to regain consciousness, telling Kagenari that ever since he came to "visit" her in the hospital, she was thinking of him. Kagenari breaks down in happy tears, glad that Madoka is awake and alive. Ex-Aid responds to Gamedeus that the will and desire to live is the one powerful trait all humans share, a power so strong that it can change fate. He attacks Gamedeus again and then finishes him off with a supercharged Hyper Critical Sparking Rider Kick. The Game Area dissolves as Gamedeus dies, who is dumbfounded how a mere human could defeat a god. Emu comments after winning the battle, "Game Clear".
Much later, Kagenari and Akemi are checking up on Madoka at the hospital. Kagenari reassures his daughter that even though she still has to see the doctor about her condition, as long as there is a future, there is hope for her. Madoka promises to be good and listen to her doctors and asks her parents if she can go to a real athletic meet this time. Akemi and Kagenari agree and Emu peers into the room to see Madoka smiling, happy he could help another patient. Asuna and Hiiro see him and Hiiro even smiles a little, proud of Emu for saving Madoka and the other patients.
As the credits roll, all the victims of Fuuma and Gamedeus's Bugster infection have recovered and are seen doing various things. Kiriya and Asuna are researching and distributing Bugster Vaccines to patients, while Kuroto is back in his arcade cabinet prison, laughing madly as he has developed an unbeatable game. Asuna changes into Poppy and shuts the cabinet off as punishment for Kuroto trying to cause trouble again. Nico is relaxing and Taiga complains about the "embarrassing" pink poster she made that promotes his clinic's examinations as she made Taiga into a roaring anthropomorphic cartoon tiger that frightens cartoon animal patients. The two comically fight about it until a patient enters the clinic, with Nico putting on her lab coat and going to the waiting room to greet the patient. Hiiro is overseeing the training of new surgeons at the hospital, who are using the Genm VR system to simulate a surgical operation. Director Kagami enters the room to inform his son the Ministry of Health needs a surgeon to operate on a patient. Hiiro smiles and says that there is nothing he cannot cut and heads out, with Director Kagami proud of his son and comically imitating him when he leaves. Emu is outside, showing some kids how to play and beat a video game. Once he clears it, Ginko Yumita storms over to the bench where Emu is sitting, scolding him for fooling around and pulling his ear as he has to get ready for his new job. Emu heads out but trips over and then gets an emergency call, Emu races off to the location of a Bugster infection.
Emu fights the Bugsters with Parado as Ex-Aid Double Action Gamer Level XX, wondering why there are so many of them. This is interrupted by the exclamation of "ARE YOU READY?" from above and the appearance of a strange red and blue Kamen Rider, who swiftly defeats the Bugsters. Emu recognizes the individual as a Kamen Rider, and the Rider, known as Build, knows who Ex-Aid is. Build then proceeds to try to use some kind of container on Emu, but Parado interferes. Parado changes into Para-DX, but Build says he has no interest in him and merely wants Emu. Build pulls out two colored bottles and changes into a "Gorilla Mond" (a combination form of a gorilla and a diamond) to overpower Kamen Rider Para-DX Lv. 99 and blocks his attacks with superior defense. A leftover Bugster tries to sneak attack Build from behind, but the Rider converts him into diamonds for his Vortex Finish attack on Para-DX. Parado is defeated and Emu's powers are sucked up into Build's clear container he held earlier. Build revels in his work, noting he has successfully extracted a Kamen Rider's essence in this "experiment" as the empty bottle turns purple and has the words Kamen Rider Ex-Aid appear on it. Emu is stunned he is no longer in Ex-Aid Action Gamer form and de-powered. Build introduces himself to the defeated duo before taking his leave, presuming that they will see each other again someday. The film ends as the screen glitched in a black backdrop with a question caption: The Game Never Ends?
