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.

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.

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.

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.

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.

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.

After being beaten by the El of the Wind, Ryo Ashihara and Shoichi Tsugami are nursed back to health by the two girls they helped.

As the Scorpio constellation continues to shift more and more people who were born under the constellation commit suicide. Makoto Hikawa believes that they die after seeing their doppelgänger.

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.