To take preventive measures against further atrocities caused by the Unidentified Life Forms, the police introduce the G3 unit. But when it is time to fight the murderous Pantheras Luteus, the G3 falls short to the power of Agito.

After the murders of the Saeki family, Makoto Hikawa decides to do some digging into the photo he found of the son, Nobuhiko. Halfway through his investigation two more "Unknowns" appear. At the same time Shoichi Tsugami, who is trying to get along with his adoptive family, falls into a trance-like state and becomes the Kamen Rider Agito.

Agito turns on G3 after defeating Pantheras Albus and Pantheras Tristis, damaging the G3's suit severely. The police have no choice but to label Agito dangerous. Shoichi Tsugami comes to grips with his situation and declares that he must "protect the place where he belongs". Ryo Ashihara finally awakens from his critical state to quit the swim team and go rogue.

The O-Parts lab finally unwound the ancient puzzle, revealing a mysterious DNA model, and they try to replicate the DNA. Shoichi Tsugami decides to leave home after being seen transforming into Agito by Mana Kazaya. Ryo Ashihara's swim coach tracks down his star swimmer and Ryo decides to "show him everything".

The O-Parts lab has been disassembeld after the DNA baby escaped, leaving more questions than answers. Ryo Ashihara, after being distanced from his swim coach, tries to get back together with his former girlfriend Mayumi Kitahira, Mana Kazaya's new math tutor, as a way to keep him grounded as he tries to figure out what is happening to him.

After being saved by Agito from the two snake Unknowns and seeing Ryo Ashihara accidentally change into Kamen Rider Gills Mayumi Kitahira decides she must put distance between herself and her former boyfriend. Seeing her leave Ryo decides to put his transformation to the test, but he must battle the monster within himself.

After defeating one of the Snake Unknowns Ryo Ashihara goes into shock due to the recoil of his powers and is abducted by the DNA child. Makoto Hikawa's supervisors feel that they must rethink Makoto operating the G3 unit and have suspended all operations of the G3-System. Makoto reflects on the incident that led to him becoming G3. Mana touches Shoichi Tsugami's head when he collapses and accidentally dives into his memory with her powers, discovering a terrible connection between him and her late father.

Mana Kazaya distances herself with Shouichi while she sorts out what she saw in his memories. Agito unleashes a new power in order to stop the Corvus Croccio Unknown from causing anymore casualties. The police department finally decides what action to take with the G3-System.

The OverLord has fully matured and vanishes, leaving a frightened Gills wondering why he should be so scared. Toru Hojo has succeeded in becoming the G3-System operator and is out to prove that he can not only defeat the Unknowns but capture Agito. Shoichi Tsugami bumps into someone who says she knowns who he is, but she seems to be hiding something dangerous.

Shoichi Tsugami has been taken into questioning for the murder of the woman he was suppose to meet, Tomoko Miura. In order to prove his innocence Mana Kazaya must use her psychic abilities to find the true culprit. Ryo Ashihara learns about his father's death, who up until now has been missing. The octopus Unknown, Mollipes Octipes, that melted after the battle with Toru Hojo, comes back to finish the job.

Toru Hojo flees the battle with the octopus Unknown after his attacks fail to work, abandoning the G3 suit and leaving Agito to defeat the Unknown. Shouichi and Mana decide to track down a friend of Tomoko Miura who may or may not know about Shouichi's past. Ryo Ashihara discovers a notebook in his father's belongings full of names and tries to figure out what his father was working on before he passed away.

Due to his excellent deduction work and saving a woman, with some help from Agito, from a pair of Unknowns Makoto Hikawa is once again instated as the operator of the G3 unit. Saeko Shinohara tells Shouichi and Ryo that there are ruins of an ancient civilization in the nearby lake and that the people of the civilization use to revere a warrior whose mark bears a similar resemblance to Agito's mask. Unfortunately, Saeko seems to have closed herself off to other people after the Akatsuki incident.

The OverLord has been declared mentally unstable and was moved from the jail cell to a hospital, where he is paid a visit by a mysterious man. At the same time Koji Kono and Makoto Hikawa walk though Professor Nobuyuki Kazaya's murder. Shouichi and Taichi try to figure out what to do for Mana's birthday.

G3 comes to the rescue after Shouichi is stung by the scorpion Unknown. The diagnosis is that Shouichi only has 24 hours to live, he decides to live out his day normally telling Makoto Hikawa that he just dosen't feel like he is going to die. Ryo Ashihara continues with the list in his father's notebook but comes up short. The G3 team takes a further look into the ball and VHS tape hidden by Professor Nobuyuki Kazaya.

With the help of The OverLord Shouichi defeats the scorpion Unknown and lives to see another day. Toru Hojo has received permission to capture Agito, but not to the extreme measures he wanted. Taichi falls ill and a woman claiming to be a housekeeper, hired by Professor Misugi for while he is away, treats him back to health.

The Misugi household's new housekeeper, Aki Sakaki, is confronted by Ryo Ashihara because her name is in his father's notebook. Unfortunately for Ryo she claims she knows nothing, but he doesn't believe her and follows her. After becoming closer to Shouichi and Taichi, Aki becomes the target of an Unknown... and Mana's wrath.

Ryo Ashihara is ever persistent and keeps pushing Aki Sakaki about what happened to his father on the Akatsuki-go. Mana still believes that Aki is not Shouichi's girlfriend but despite her wishes Shouichi becomes enticed with the idea of having a girlfirend, even if he can't remember her. Toru Hojo puts his team in place to capture Agito, but will it be enough?

Kamen Rider Gills is left for dead after being assaulted by Toru Hojo's firing squad and G3's attack. Shouichi decides to live at Aki Sakaki's house while she's gone. Due to the lack of progress in anti-Unknown defense the police decide to bring in Toru's ex-partner Ryuji Tsukasa to head the G3 team.

Shouichi decides to take over the bakery he works at when his boss, Sashi Hanamura, is murdered. Ryuji Tsukasa convinces the police department that the current G3 team should be disbanded and a new one should be made with him at the helm. Toru Hojo figures out that Hanamura's death was not caused by an Unknown but by a human making it look like an Unknown.

Ryo Ashihara remains in critical condition but is being cared for by Shoichi Tsugami. The OverLord imparts a portion of his power to Tetsuya Sawaki after Tetsuya sees what humanity has to show him. Aki Sakaki's powers awaken nine months after the Akatsuki-go incident. She uses her new found powers to hunt the members of the Agito Capture plan.

Thinking that Ryo Ashihara is dead Aki Sakaki goes after the Agito Capture team for vengeance. Ryo awakens to a voice in his head and finds Shoichi Tsugami living in Aki's house. With proof of people who have supernatural powers the G3 team starts connecting the dots to why the Unknown attack people.

Seeing Aki Sakaki dead in the hands of Agito, Ryo Ashihara mistakenly believes he killed her and attacks Agito as Gills. Agito, Gills, and G3 have a heated battle resulting in the G3-System being damaged far beyond repair. After the battle the police department say that the new G3-System, G3-X, will have to compete against Toru Hojo's new system, the V-1 system, to see what suit will be used against the Unknowns in the future.

After his body is pushed to the limit Makoto Hikawa is forced to give up his position as the G3-X operator. Sumiko Ozawa feels that Makoto uses too much force and that he will not sync with the G3-X's AI system, she instead needs a much more relax and carefree person... like Shoichi Tsugami.

After going berserk, destroying the V-1 system and the second bee Unknown, and then attacking Agito, Makoto Hikawa faints in the G3-X system. He is hospitalized and comes to the realization that while the G3-X system is perfect, he has many flaws. Makoto turns to the only other person he sees as a suitable candidate for the G3-X, Shoichi Tsugami.

Makoto Hikawa takes full responsibility for going berserk after seeing Shoichi Tsugami effectively deal with an Unknown in the G3-X suit. The police cheifs recognize this and decide to have Toru Hojo operate the G3-X once the V-1 system is disbanded. Sumiko Ozawa must come to grips that her G3-X system is too perfect and too smart and in order for Makoto to operate it she must make it flawed. Ryo Ashihara is fully healed and looks for revenge against Agito.