Emu, a clumsy pediatrics intern takes young Sota, who is suffering a mysterious illness, to the announcement event of the latest "Mighty Action X", Sota's favorite game. Emu became a medical doctor in order to save someone's life because his life had been saved once through surgery. However, a mysterious virus emerges from Sota's body and the event turns into chaos. Emu hears from Asuna, an employee of the Ministry of Health, that transforming into a Kamen Rider can save the patient. Emu takes on this "operation" and inserts the Mighty Action X Gashat into the Gamer Driver, transforming into Kamen Rider Ex-Aid!

Becoming Kamen Rider Ex-Aid, Emu now must serve as both a pediatrician and a member of CR. A gifted surgeon named Hiiro Kagami comes back from the United States and is not only the son of the director, he’s also Kamen Rider Brave. This results in a clash of ethics when it comes to dealing with patients.

Emu follows a patient who’s fled in fear of a doctor and encounters Taiga, who transforms into Kamen Rider Snipe. Once Emu learns of the past connection Taiga had to CR, he visits the dark hospital Taiga resides in to rescue the patient.

Emu cannot transform into a Kamen Rider since Taiga stole his Gashat. Medical Examiner Kiriya Kujo appears before a crestfallen Emu. He brings a Bugster-infected patient and offers to steal back Emu's Gashat in exchange of helping Kujo out with his prodigious gaming abilities.

When the thief of the 4 new Rider Gashats is infected with the Bugster virus, Emu and Hiiro clash about saving his life or not, and the identity of the mysterious Kamen Rider that is attacking the others is finally revealed.

The girlfriend of the student that the Bugsters were after has contracted the Game Disease. Hiiro transforms into Brave and succeeds in separating the Bugster from the girl.

A hospitalized patient showing two symptoms of the Game Disease has appeared. Emu and Hiiro transform and succeed in separating the two Bugsters from the patient. But Genm appears again to interfere, letting the Bugsters escape.

Taiga manages to capture the Bugster which escaped in the last episode and obtains the Jet Combat Gashat, holding the Bugster, and thus the patient, hostage in exchange for the other Riders' Gashats. When they arrive to challenge him, he decides only he is needed to fight the Bugster, and tries to destroy Ex-Aid and Brave.

Graphite infects the Deputy Director-General of the Ministry of Health with the Bugster Virus, while the doctors at the CR fall out over the most important course of action: Save the Patient or defeat Graphite?

Unable to control the powers of the new "Drago Knight Hunter Z" Gashat only by himself, Emu discovers that to do so he must convince the other Kamen Riders into join forces with him. Once he tricks them into doing so, the time comes for their showdown with Graphite.

Emu gives Kiriya another chance to earn his trust. Kiriya then takes the chance to finally reveal Kuroto's intentions and expose him as the Black Kamen Rider that is working with the Bugsters.

With Christmas around the corner, Emu runs against time to defeat the Salty Bugster again and save another patient, while Kiriya's investigation leads him closer to the truth, but his life is in danger when he faces Kuroto's new power.

With the Bugster infection spreading rapidly, the authorities can't hide the disease from the public anymore. After Kiriya's death, Kuroto starts targeting the other Kamen Riders for their Gashats, but Parad approaches Emu, offering him a blank double Gashat which will allows him to attain a new level of power…

Ex-Aid, now as two, get into an argument about defeating Genm or the Aranbura Bugster. They both seem to be Emu, but Genm and the Bugster take this opportunity to escape. Emu reverts to his human form and falls unconscious. Wanting to save Dr. Shirakawa, Emu asks Hiiro to perform a surgery on his cancer. He has his Gashat back and faces the Aranbura Bugster to also cure Shirakawa's game illness. Will the surgery succeed? What will happen to Ex-Aid?!

Taiga tries to find out more about Emu's infection, and starts to discover the secret that might be why Kiriya was killed. Meanwhile, using data collected from fights with Mighty Brothers XX, Parad makes his move and reveals his new form: Kamen Rider Para-DX Level 50.

Emu thinks Taiga and Hiiro attacked him since he is the source of stress for Nico, who is suffering the Game Disease. He does not realize the true intention of the other two riders is to eliminate the Bugster virus residing in Emu himself, who is unknowingly infected with the disease as well. Brave attacks Ex-Aid again but Revol Bugster and some grunts appear to…defend Emu! He is further convinced he is the source of Nico’s stress. Genm Level X appears and attacks both riders. He succeeds in stealing all of Hiiro’s Gashats and seems intent to do the same with Emu’s.

A lovable hamburger Bugster named Burgermon appears. Emu transforms into Ex-Aid, but attacking it causes the game disease patient to suffer from stress. What is this? The CR accommodates an employee of the Genm Corporation’s development department. A game called Ju Ju Burger is under development with a game virus infection, and Burgermon seems to be separated from the game. Burgermon acts like an adorable child; he doesn’t seem so bad. As expected, Emu will have to deal with what’s in control of his head.

"Hiiro, are you hiding something from me?" Emu calls out Hiiro on the roof of the hospital. In the last battle, Genm tells Emu that he saved the Bugster because his body told him to do so. Emu also suffers from serious headaches after every transformation since creating the Mighty Brothers XX Rider Gashat. And most of all, Emu is incompatible with the surgery and yet he can still transform into a Kamen Rider. Everything is starting to come together, so what will Hiiro's response be? Meanwhile, Kuroto Dan returns to Genm Corp., and using the Gashacon Bugvisor, he begins to spread the Bugster Virus...

Emu finally learns of the horrifying truth that he has the game illness. The Bugster virus in him acts up and he collapses to the ground, though for some reason no Bugster has appeared... Emu later wakes up in CR with his personality completely changed to that of "Genius Gamer M". When a new Level 30 Bugster emerges, Emu transforms into Ex-Aid with delight, and fights as if he were playing a game while no longer concerning himself with the patient. Just what has happened to Emu?

Taiga and Nico meet a high school student named Daisuke who is infected with the Bugster Virus and calls both Emu and Hiiro for their help. Parado suddenly appears and Hiiro faces him in his new form while Emu is hesitant on joining the fight.

Emu and Hiiro learned from Poppy that Kuroto was the one who had suggested Emu to CR. Meanwhile, a police detective is investigating the Zero Day case, causing him to interrogate Kuroto's father, Masamune. During the investigation, he gets infected by the Game Illness. In order to save him, Emu confronts Masamune.

Kuroto falls victim to the Bugster virus and is aprehended by the authorities. Despite everything Kuroto did to him and his friends, Emu is determined to treat him, but the others are wary, wondering if saving Kuroto's life is worth the effort, or even if he will be grateful for it. On the other sides, Hiiro finds some very useful information from Kiriya Kujo's belongings while Emu receives an emergency call that a Bugster is rampaging on a certain location.

Recovered from his infection, Kuroto resumes his plans to complete "Kamen Rider Chronicle" and the members of CR seem to have no way to stop him, until Taiga gives Emu a new Gashat that brings forth a power never seen before.

The fierce battle between Ex-Aid and Genm has now come to an end. Meanwhile, a woman who was injured, Sora, is brought to Emu and Hiiro. Sora's band members argue, when suddenly all 3 of them are taken over by Bugsters! And on top of that, when Emu tries facing them alone, a young man appears yelling, "Yossha Lucky!"

Recently, Emu has been feeling a little worried. He is very quiet and hasn't talked much since Poppy Pipopapo suddenly disappeared. Just then, Hiiro is shocked by the sheer number of emergency calls coming to CR, all reports of the game illness! As the only CR doctors, Emu and Hiiro rush to the indicated locations, but what they find there is an unbelievable sight...

Kamen Rider Chronicle has already begun! Para-DX has joined the game and defeated the first round of the general players, giving them a Game Over as Emu watched them disappear before him. Kamen Rider Chronicle is being sold at an extremely fast rate, which catches the attention of the Ministry of Health. To avoid any form of confusion, Kyotaro Hinata orders a temporary halt on the actions of the doctors in CR. However, a game disease patient escapes from CR in an attempt to cure his own game disease, which leads Emu to chase after him. Then suddenly, Poppy Pipopapo appears before them with a new Driver and a Rider Gashat of her own…

Thanks to the public announcement by the Ministry of Health, the number of Kamen Rider Chronicle players seems to have decreased significantly, which would subsequently reduce the amount of game disease patients. However, unbelievable information about Kamen Rider Chronicle is released by Ren Amagasaki, the new CEO of Genm Corp. There is a hidden component inside Kamen Rider Chronicle, one that is said to dramatically increase player participation! However, Taiga, who was suspicious of the love and go CEO's actions, goes into Genm Corp. to confront him himself...

Emu managed to notice Poppy smiling after the Rider's battle against Lovelica. With her sudden change of heart, Emu believes that she was suddenly swept up in all the commotion. Although he was attacked by Kamen Rider Poppy, Emu does not believe she is a bad Bugster. When Kamen Rider Chronicle starts up once again, Poppy Pipopapo is summoned. When Emu confronts her, he shouts "You aren't like this!" to her, just as she appears to deliver the final attack at the Riders who violated the game...

It was Emu who managed to return Poppy Pipopapo back to normal thanks to the bond they share, but it was not a time for relief. Suddenly Parado begins to manipulate Emu! "Let's do this, the most exciting of all games!" Emu managed to remove the Gashat Gear Dual that transforms Parado into Kamen Rider Para-DX and uses it himself! Just what on Earth is going on?! Finally, the points connecting Emu and Parado are beginning to reveal themselves...

Ex-Aid, Brave, and Snipe have all been defeated at the hands of Kamen Rider Para-DX Level 99! Also, Parado begins to manipulate Emu's body as his own in order to retain the infection. Much to the other Rider's surprise, Poppy brings out another Proto Mighty Action X Gashat and a Gamer Driver! Poppy had found them thanks to her revived memories of a young Kuroto. What is the meaning behind this Gashat? Poppy manages to use the power of Level 0, in the hopes of bringing Emu back to normal...

No one can hide the fact that they are upset about Kuroto's revival. How was he able to return? What is Kuroto's true intention by making this Continue a reality? Meanwhile, Emu cannot forgive what Kuroto did to all those patient's lives. He realizes that in order to eliminate Kamen Rider Chronicle, his cooperation is required, but Emu is getting tired of his attitude...

Ex-Aid and crews have gained the right to challenge the advanced Bugsters in order to clear Kamen Rider Chronicle. The three advanced Bugsters are Parado, Graphite, and Lovelica. The time of the final battle against the four Kamen Riders is at hand! At last, the curtain rises on the scene of the last battle! However, a disturbing darkness suddenly begins to appear...

The fact that Hiiro has betrayed Emu weighs heavy on the members of CR. If Hiiro is working with Masamune, then there can only be one reason for it. With everyone on the ropes about the situation, suddenly both Parado and Graphite show up in CR! To counter against Cronus, they ask Kuroto about Kamen Rider Chronicle's final boss, Gamedeus, the only being who can defeat Cronus. Just then, Brave confronts Ex-Aid as he is responding to an emergency call...

Apparently Hiiro wasn't the only accomplice that Masamune had in the palm of his hand! Cronus suddenly summons Kamen Rider Lazer Turbo Level 0 into the fight! In order to further expand the presence of Kamen Rider Chronicle around the world, Lazer Turbo stands before the Doctor Riders in an attempt to keep them from ending the game! Much to the shock of everyone, Kamen Rider Lazer Turbo finally reveals his identity...

Genm Corp. announces a new addition to Kamen Rider Chronicle, the "Cronus Capture Quest", and despite knowing what dangers lie ahead, countless new players join the game! Meanwhile, Emu is still reminded of the message Kiriya said to him before Masamune took him away. Kuroto completes an invincible golden Gashat holding an unbelievable amount of hidden power! Ex-Aid and the others rush to stop the "Cronus Capture Quest" as Brave and Lazer Turbo stand in their way once again...

Ex-Aid finally went Muteki and was able to beat Cronus! Masamune, who does not like the fact that Ex-Aid was able to attain a power that exceeded his control, angrily forces Hiiro to work for him as he claims Saki as a hostage! Brave forcibly renews his resolution, and this time he is able to transform into Legacy Gamer Level 100! Emu is more confused than ever, while Taiga is the only one who truly understands just how painful Hiiro's decision truly is…

Graphite mercilessly attacked the body of Taiga which forced him out of his transformation! The injured Taiga has been rushed to the hospital immediately, but there is a high possibility that his heart has been damaged. Moreover, it seems that it would take an expert-level of surgical expertise in order to save his life. After returning to Masamune, Hiiro's father and Asuna make an urgent phone call. The director asks Hiiro to perform Taiga's surgical operation. Just what decision will Hiiro come to in the end?

In order to deprive Ex-Aid of his transformation abilities, Cronus decides to target Parado directly. Para-DX without Emu is still not perfect, so he is beaten easily. Even so, Ex-Aid cannot stop chasing Cronus. However, Cronus was planning an underhanded scheme. Nico's game disease, which just started to show symptoms, belongs to that of Gamedeus, the Last Boss of Kamen Rider Chronicle! In order to defeat Gamedeus, Ex-Aid has to defeat both Graphite and Parado! Just then…Parado's hands begin to shake violently…

Parado has been defeated, and Emu has lost the ability to transform into Ex-Aid! Following Parado's annihilation, the other Riders team up in order to defeat Cronus. Brave, Snipe, Genm, and Lazer Turbo, all alternate the Hyper Muteki Gashat in order to counteract Cronus' Pause. Meanwhile, Emu was deep in thought. The fear of death that he felt at the moment of his extinction, even if he was a Bugster, he shared the same feeling as he did in that moment. Just then, Emu takes out the Mighty Brothers XX Gashat…

Kamen Rider Chronicle has been reset thanks to Masamune's special ability! Thanks to his Bugster infection, his hidden power has awakened, and the game is reset to the moment before Emu received the Hyper Muteki Gashat! Finally, with Parado having already been defeated, Graphite is the only game character left in order to clear Kamen Rider Chronicle! Brave and Snipe both challenge Graphite with a burning fighting spirit. Meanwhile, Emu believes that Graphite infected with Gamedeus' virus may be the only one strong enough to defeat Cronus. However, Graphite refuses to cooperate with the Riders…

The Last Boss of Kamen Rider Chronicle, Gamedeus, is finally born! If you defeat Gamedeus, then the game will end! However, at the moment of Gamedeus' revival, massive amounts of the Bugster Virus spread throughout the city! The number of infected patients are increasing, as well as the number of people being rushed to the hospital. While the doctors attend to the patients, Ex-Aid and Para-DX team up to fight Gamedeus! But their strength is far too weak against Gamedeus, as he sends them flying easily. At the same time, two people were confronting each other. Kiriya and Kuroto, both transformed, clash fists to see who's fate will be decided in the end…

Suddenly, the Gamedeus virus begins spreading through the streets! Masamune becomes Gamedeus Cronus and appears before the other Riders, as he summons Nico into the World of Kamen Rider Chronicle! Nico is the one who is qualified to challenge the Last Boss of Kamen Rider Chronicle as a Ride-Player, but it seems clear that Masamune is going to try to Game Over the player who is closest to beating the game in order to reset it. In an attempt to save her but unwilling to let the others follow, Taiga uses the Chronicle Gashats seized from patients and goes to find her. However, the other Riders cannot enter the World of Kamen Rider Chronicle! Just what will happen to Nico's fate?

Gamedeus Cronus has grown massive and become the strongest Last Boss! The Gamedeus Virus expanded and the pandemic has gotten worse. The Gamedeus Virus can now be transferred from person to person, turning the infected into Bugster Virus foot soldiers! Two Bugsters witnessing this symptom, Parado and Poppy Pipopapo, decide to take action. "There is something that only us Bugsters can do…" Poppy says as she rushes to Ex-Aid…

Though Gamedeus was finally destroyed at the cost of Poppy Pipopapo and Parado when they extracted the Bugster from his body, Masamune Dan survived and takes advantage of Emu no longer being able to use Hyper Muteki. The Kamen Riders are at a huge disadvantage, while Cronus doesn't hold back, and initiates Pause. All of the Kamen Riders' movements are frozen in time, and he prepares to kill them, starting with Emu…