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.

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.

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.

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.