Having lost his parents to the Crusades, Zato was taken in by the Assassin's Guild in 2166. As an underling, Zato presumably witnessed the guild's swift expansion and deviation, Slayer's resignation as leader two years later, and the organization's subsequent decay. In 2173, Zato, disgusted with his own powerlessness, risked death by invoking the forbidden arts. He lost his eyesight, but with his newfound powers, he became the guild's leader within weeks.
That same year, Millia Rage and Venom were taken in by the guild. To them, Zato was their savior and teacher; Zato earned Venom's undying loyalty, and eventually fell in love with Millia—the two becoming Zato's right and left hands, respectively. As leader, Zato had the guild turn to money contracts, but attempted to turn it into a place where those with nowhere else to turn after the war could take shelter; however, the Guild had become too massive, making change difficult.
When the guild was hired to assassinate Duke Dorian Scaburi of Castellia, the mission attracted Slayer's attention, who tested Zato for the changes to the guild. His meddling led to Millia's capture by Leon Mining. Zato—unaware that Slayer would release Millia of his own accord—agreed to assassinate King Saltelia I to save her. Yet, as they were about to kill the king, Millia stabbed Zato, leaving him for dead, and snatched the baby away to protect him. Despite his wounds, Zato escaped Mining's ambush and met with Slayer under a poplar tree outside the castle. They were soon surrounded by Mining's forces, but thanks to Millia and Venom's intervention, Mining was defeated. Zato spared his life, Mining then becoming his ally. In spite of her betrayal, Zato forgave Millia and let her find foster parents for the king instead of inducting him into the guild.
Sometime later, Zato, Millia and Slayer would later cooperate again in the Mount Rosa Operation. In 2177, Zato was hired to "take care of" Dr. Baldhead, but Zato ended up killing his patient instead, ruining the doctor's life by making him think he had committed malpractice. Then, in 2178, Zato led a high-risk operation, but Millia—secretly working with the IPF for her acquittal—betrayed him and took the opportunity to flee. Her escape threw the assassins into chaos, allowing them to be caught red-handed. Zato was arrested and put in a barrier prison, where his affection turned to hate.
Languishing in the utter blackness of his prison, a tall, thin figure appears before him. He asks Zato if he wants out of there, and if he has a pressing appointment with a woman. Zato wonders how he knows of Millia, but the figure says that if he wins an upcoming tournament, he will be free to punish her. While suspicious, Zato agrees to the offer, having nothing to lose.
Manipulated by Testament like the others, the bloodshed from the tournament releases Justice from her seal, but she is promptly killed by Sol Badguy. However, the constant battling takes its toll on Zato. Having demanded too much of his curse, Zato's shadow begins to move by itself and tells Zato that he can no longer control him. The shadow thanks his host for incubating him, and takes possession of Zato's body as Zato calls for help.
In 2181, while seeking its brethren, the shadow—who calls himself Eddie—begins to follow the scent of the Gear with free will, Dizzy. In one path, Eddie taunts Millia, who learns that Zato has been taken over; after a fight that results in her defeat, she dares him to finish the job, but Zato resists and rips Eddie off though it will kill them both, in an act of repentance. In his other path, Zato implores Eddie not to harm Millia; the shadow simply takes her hair, his "comrade" and fellow weapon.
His life force eroded due to involuntary overuse of the shadow, the physically-weak Zato perishes, but by then Eddie is almost completely in control, and keeps on using Zato's body as his own.
Yet, Zato's body continues to deteriorate and Eddie consults with Faust. Without Zato's soul, his body's cell structures are disintegrating in prevent him, a weapon, from becoming independent. Per I-No's manipulations, Eddie thus begins to search desperately for another host. His efforts are in vain, however, and he soon follows Zato into the afterlife, presumably buried by Millia.
Zato's remains were confiscated by the Conclave, and he was subsequently used as a "guinea pig" to develop the Art of Resurrection, with Baldias conducting the research. By September 3, 2187, Zato and Eddie are revived, and then confined in a dimensional prison. Rendered a shell of his past self, Zato makes no attempt to escape despite Eddie's prodding until he senses that Millia is nearby on October 14. Upon emerging, Zato finds himself before Millia and Venom at the Opera House, soon joined by Slayer. Zato asks Venom to protect her while he tries to locates the Conclave. Before his departure, Faust appears to settle the "mistake" that ruined his life; Zato says that he can kill him if he wishes but he needs a little time before that, revealing why the Conclave targeted the doctor.
On October 28, Zato's quest takes him before Ramlethal Valentine; with the Cradle's activation, he attempts to locate Ky Kiske to pass the intel he possess, but is unable to. He thus returns to his fellow assassins' side, only to find that they were attacked by Bedman and taken to Uighur. Zato attacks him for harming Millia, thus saving Chipp Zanuff, and Bedman disappears, recalled by his ally. Afterwards, per Slayer's suggestion, Zato goes to Zepp and meets with President Gabriel. On November 1, Ky and Sol arrive, and Zato is able to disclose that the Conclave intends to use the art of resurrection to revive Justice by binding Chronus's soul to her body.
With the Conclave's defeat and the Universal Will's looming threat, in hopes of rebuilding the guild, Zato is sent to make a offer to King Daryl, who by November 7, accedes to the assassins enlisting as "soldiers". At Slayer's mansion, Zato relays this to the others; they all decide on the elimination of Bedman as a symbolic requirement, with Venom taking it upon himself to be the sacrificial lamb for legitimacy and recruiting Robo-Ky to help him. Meanwhile, Zato tests his own accuracy in tracking down Bedman and takes Slayer and Millia to a wasteland; there, Slayer briefly engages Bedman in a revenge match, but they soon leave.
During the battle at the Illyrian capitol, Zato, Millia and Slayer lead the guild in defending the capitol from Ariels's forces, the Phalanx and massive Gears. As they struggle, Zato asks why Slayer saw light in him, and the vampire reminds them both of the Mount Rosa operation, rekindling their convictions. Ultimately, the Illyrian main team defeats Ariels and Jack-O' Valentine merges with Justice. Meanwhile, Bedman is defeated by Venom and Robo-Ky, who sacrifices his body to do it; Venom, however, survives, but is declared dead.
In the aftermath, Zato takes it upon himself to "eliminate" Venom, their loose end due to unintentionally surviving his battle with Bedman. Zato has 2cave test Venom's resolve and make him choose between protecting the town or rejoining the "wolves"; having chosen the first, 2cave gives Venom, on Zato's behalf, a deed to a bakery so that he may live a normal life incognito while trying to restore Robo-Ky's body. Zato later visits them.
In the following weeks, King Daryl reinstitutes the Post-War Administration Bureau, hiring the assassins due to their skill at informational warfare, with Millia as its director, to support the Illyrian government. About three weeks after the battle, upon the U.S. agreeing to That Man's involvement at the G4 Summit, they request that all nations involved help with security.
Daryl thus calls Zato and Millia as specialists to investigate the White House. They report to the Illyrian War Room to inform Daryl and Leo Whitefang of their findings, although the latter is reluctant at the assassins' recruitment and methods. Zato and Millia tell them of a "black box" they found before Daryl departs for the summit. Unbeknownst to them, Happy Chaos hacks into their files. After the summit starts, Zato tells Leo why the assassins have changed their ways—to "remain human"—, and Leo warms up to them both. He also decides to leave the box be, but then Zato realizes they have been hacked.
Meanwhile, Chaos takes Daryl and the other representatives hostage and launches all missiles in the world. Zato manually deactivates the castle's weapons, while the other missiles are deactivated mid-flight by the dignitaries themselves. Upon a link being established between Sol and Vernon at the White House, Zepp, the Pentagon and Illyria Castle, Chaos activates the White House's Tír na nÓg mode. Zato then helps analyze the black box and facilities. Despite their joint efforts, Chaos ultimately uses That Man's Tome of Origin to restore I-No to godhood. As with the rest of the world, Zato witnesses as I-No starts a process to grant humanity her same powers, but she is soon defeated and seemingly killed by Sol, Ky, and Nagoriyuki. In the aftermath, Zato, Millia, Leo and Ky reflect upon the future I-No wanted. Sometime afterward, Zato takes Millia to see Robo-Ky and Venom at his bakery.
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