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.

Agito is defeated by Gills, leaving him to drown. Shouichi doesn't die but regains his memory and then proceeds on a trip to find out just who the real Shoichi Tsugami is. Ryo Ashihara continues to work down the list of names in his father's notebook, meeting Aki Sakaki's "friends": Masumi Sekiya and Katsuhiko Sagara.

After being saved by Ryo Ashihara, Masumi Sekiya and Katsuhiko Sagara decide that Gills possesess too much of a threat to them and must die. Shouichi and the real Shoichi Tsugami meet face-to-face and talk about their one common link: late sister and girlfriend Yukina Sawaki, who was one of the first people with powers and committed suicide.

A few weeks before Episode 27... A boy running from his past, and two men in black suits, bumps into Ryo Ashihara. Ryo decides to help the boy run far away... until they run into an Unknown.

A victim of an Unknown attack happened to be a safe cracking thief whose accomplise was his younger brother. The police figure that if they can find the younger brother than they can protect and arrest him. Makoto Hikawa recruits Mana and Shouichi to help in the effort.

Toru Hojo decides to take Nobuyuki Kazaya's murder case saying that it wasn't an Unknown that killed him but a human with telekinetic powers. Tetsuya Sawaki, going against the OverLord's principles, tries to revive Ryo Ashihara using a super powered human. Unfortunately, the man who killed him, Katsuhiko Sagara, is not powerful enough to do it.

After attacking the tennis team at the fireworks display Mana believes that she unknowingly killed her father. Mana tries to distance herself from the people she loves and gets kidnapped by Katsuhiko Sagara, who hopes that she can make a future safe for people with supernatural powers.

Mana, under the guidance of Tetsuya Sawaki, starts the process of reviving Ryo Ashihara and it seems to have a backlash on her body. Shouichi tries to reach out to Mana who's run away from home, showing her that she's not alone in trying to find "the place where they belong".

The El of Water has possessed Masumi Sekiya and it's reviled that it killed the two Akatsuki-go members from Gills' Resurrection in her body without her knowing. The El of Water has now turned its sights on Agito. Shouichi comes face to face with the El of Water and believes no matter what he can't defeat it, becoming scared. He starts to question why he became Agito.

After being beaten by the El of Water both Gills and Agito retreat. Shouichi becomes bedridden with injuries and Ryo must protect him even though both of them known they are no match for the deadly Unknown. One of the last remaining survivors of the Akatsuki-go incident, Koji Majima, becomes targeted by a mantis Unknown.

Shouichi, fighting for himself, transforms into Agito Burning form and defeats the mantis Unknown and the El of Water. The El of Water, in a last ditch effort, retreats into the OverLord's body and vows vengeance against Agito. Shouichi regains his self-esteem and rejoins the Misugi household. Ryo Ashihara witnesses someone being attacked by an Unknown and goes to save her, he encounters a strange man in black named Kaoru Kino.

Kaoru Kino saves Ryo Ashihara and Koji Majima from an Unknown. He tells Ryo that his sole purpose in life is to save people, either as a doctor or as Agito. But can this man, haunted by his past, really be trusted? Makoto Hikawa finally figures out that the Unknown are targeting the people that he once rescued but doesn't know why.

Kaoru Kino hunts down and brutally injures Ryo Ashihara, claiming that the world only needs one Agito. As Koji Majima and Ryo flee Kino turns back into a human from Another Agito and is seen by both Makoto Hikawa and Toru Hojo. While Makoto is truly thankful that Agito is a "pure" person, Toru believes that he can once and for all capture Agito when he transforms back into a human.

Shouichi is captured by Toru Hojo on accident when leaving a battle with an Unknown. Toru takes him in for questioning even though Toru saw Kaoru Kino transform from Agito previously. Ryo Ashihara, who escapes from the murderous scalpel of Kino, finds himself once again hunted by Another Agito.

Agito and Another Agito battle and come to a draw, allowing enough time to let Ryo Ashihara, Koji Majima, and Makoto Hikawa escape. Tetsuya Sawakii meets Koji and Ryo and tells Koji that there is only one way to save Ryo... to transfer his seed of Agito to Ryo. Toru Hojo and Sumiko Ozawa report to their superiors that Shoichi Tsugami is Agito and that he should be allowed to act freely. Their superiors decide to keep this fact a secret leaving Hikawa to wonder about who is Agito.

Ryo Ashihara awakens a new power, Exceed Gills, and manages to severely damage Another Agito but decides not deal the finishing blow. Makoto Hikawa, now knowing the identity of Agito, doesn't know how he should face Shoichi Tsugami.

Shoichi Tsugami and Makoto Hikawa have finally created a good fighting bond and their relationship is back to normal. Shouichi feels that it is best to figure out why Kaoru Kino attacked them is to talk to him and figure out why he is living in the past. The El of Water has finally recovered and seeks to eliminate all the Riders once and for all.

Shoichi Tsugami has fallen unconscious during the fight with the newly evolved El of Water and all the pieces of his memories on the Akatsuki have put themselves together. Meanwhile, Mana uses her powers to translate the letter found by Toru Hojo and learns the history behind the Overlords of Light and Darkness and the origin behind the seeds of Agito.

Agito unleashes his Shining Form and combines his strength with the other Riders and defeats the El of Water. The OverLord of Darkness realizes that Agito's power has become too strong and he must deal with the Riders directly to save his beloved humans.

After Kaoru Kino's seed of Agito is stolen from him the OverLord of Darkness turns his sights on Ryo Ashihara, looking to take Gills' power. Shoichi Tsugami and Mana Kazaya go to Toru Hojo for answers about Mana's father's murder but is the truth they uncover more than they can handle?

Thanks to Ryo Ashihara, Shoichi Tsugami escapes from the OverLord of Darkness. Shouichi begins to question what it means to be Agito now that he believes that his sister killed Mana's father. Makoto Hikawa is released and back on duty. Unfortunately, he is still suffering from a severe concussion.

Shoichi Tsugami takes solace knowing that he is no longer Agito and that he is free from a fate that could be much like his sister's. But with Agito, Gills, and Another Agito out of commission who will save Mana when she is attacked?

One month later, there have been zero sightings of Unknowns so the police decide to temporarily disband the G3 team with the hopes that this whole mess is coming to a close. Shoichi Tsugami and Ryo Ashihara find jobs and try to once again have normal lives. The Overlord, seeing his beloved humanity turn on him, decides it is time to start over.

A string of strange suicides are occurring where all the people are Scorpios. Makoto Hikawa doesn't believe that these deaths are just coincidences and decides this needs further investigation. Shoichi Tsugami tries to help a female apprentice struggling to be a full time chef, believing that he can help her follow in her father's footsteps. Ryo Ashihara tries to convince a girl that there is more to life than just racing her bike.

The G3 and G3-X have been dispatched for the purpose of protecting Unknowns. The police believe that a race of Agitos will one day overthrow humanity so why not have the Unknowns kill them before it happens.

With people killing themselves because of the OverLord and two Els killing people with the Seed of Agito the Kamen Riders must unite their strengths to save humanity from extinction.