Kagato is the former assistant of Washu Hakubi, the greatest scientific genius in the universe, assisting her in the creation of her daughter Ryōko, her battleship Ryo-Ohki, and in the building of the massive battleship, Sōja. Kagato has largely the same superhuman abilities as Washū and Ryōko, though whether he was born with these powers or achieved them by genetically altering himself was unclear until the release of the True Tenchi Muyo! novels (see the True Origins section below). Kagato caught word of a historical artifact, one said to hold the "greatest energy in the universe." Ambitious with an amoral curiosity, he imprisons his mentor within her own ship, taking credit for her creations, taking Sōja for his own, and using it to pillage the galaxy (Washū would remain in his captivity for the next five thousand years). While not a psychopath who kills for the sake of killing, Kagato is not concerned with mortals or their feelings, considering them "worth nothing more than dust." They have their occasional use as tools, but are overall beneath his notice and not worth killing. However, he will not hesitate to kill should they offend him or if it coincides with a greater purpose. Those caught in the collateral damage of his "scientific methods" are similarly out of luck.
Having a powerful psychic hold over Ryōko through the gems, which are her energy source, Kagato uses her as his puppet to execute his orders, sending her on archaeological excavations as he scoured the universe for hints on his own. Once observed, a location would be razed - whether it be populated or not - lest someone else replicate his research. In all, 3,326 ruins were destroyed, with great loss of life and innumerable cultural artifacts stolen. It was during this time Kagato earned the name "Ruins Buster" and a place on top of the Galaxy Police's Eternally Wanted List. Slaves under a ruthless space pirate, Ryōko and Ryō-Ohki were recognized as major threats themselves.
Eventually, Kagato found the power he was searching for was linked to the imperial planet Jurai and its Royal Family bloodline, and Ryōko was sent on an errand to retrieve it. While successful in infiltrating the planet's defenses and nearly decimating it, Ryōko failed, and was pursued from the planet by the Prince Yōshō Masaki Jurai. Their psychic link severed - thanks to Yōshō confiscating the gems and affixing them to his sword's pommel - Kagato leaves Ryoko for dead and commits to the exploration and collection of relics on his own, destroying whatever might obstruct his goals.
Seven hundred years later, Ryōko is accidentally awakened by Tenchi Masaki, the grandson of Prince Yosho, who gives her one of the gems to wear on her left wrist (though she had asked for all three) in order to summon Ryō-Ohki; the psychic link restored albeit weakened, Kagato sets course for Earth to reclaim his "property." Once there, he is pleased to find Ryōko has unwittingly collected all that he desires - Jurai's heir (Yōshō), and its princesses, Ayeka and Sasami. He kidnaps Ryōko from Tenchi's home and greets the rescue party with mock geniality, sarcastically placing the trouble on Ryōko before Tenchi steps in with his sword. Seeing it as the key to unlocking the great power he'd sought, Kagato warns the boy not to swing around others' property so lightly, telling Tenchi to give up the sword and not his life. He is fascinated when Ryōko intervenes, wondering what she could ever see in the boy. Kagato reasserts his control over Ryōko (Kagato's control manifests itself in Ryōko's eyes; when she possessed all three gems her eyes glowed red, but with only one gem the whites of her eyes became light green, the same color as Kagato's sword) and has her take Tenchi hostage as he interrogates; Ayeka, Sasami, and First Class Detective Mihoshi Kuramitsu stand by as Kagato wonders if Tenchi is aware of the sword's power and whether the boy is suitable to unlock it.
Tenchi is able to break free from Ryōko's grasp and attacks, but does nothing but nick Kagato's cheek (which quickly regenerates, but not before drawing greenish blood). Angry, Kagato engages the boy in swordplay to test him, and is sorely disappointed by the result. Reaching out for the sword, he is kept from collecting his treasure by its true owner, Yōshō; the two fight a fairly even match even with the enslaved Ryōko attacking in tandem. After severing Ryōko's left hand, freeing her of her gem and Kagato's control, Yōshō throws the weapon into his royal tree. Thinking his rival has given up, Kagato tries to retrieve it for himself, and is quite literally shocked when he grasps the sword handle: he is not ordained to be its owner. Realizing Tenchi is the sword's successor, Kagato teleports with Ryōko back to his ship, bidding the group to improve their skills as he'll be waiting for them.
He makes good on his word, attacking Ayeka, Tenchi, and Mihoshi from Sōja as they approach in a hybrid of Ryō-Ohki and Ayeka's Royal Treeship, Ryu-Oh, all the while wondering why such fools would throw away their lives for someone as worthless ("defective") as Ryōko. During the onslaught, Tenchi attempts to use the ship's Light Hawk Wings as a weapon rather than their intended purpose as defense, and it proves costly as they are overwhelmed; the bottom half of the ship is destroyed, with Tenchi caught along with it.
Believing Tenchi to be dead, Ryoko is able to free herself and mounts a last ditch effort for revenge with the others, not caring if she kills herself so long as Kagato dies with her. She and Ayeka personally engage Kagato, as Mihoshi gets lost along the way and accidentally frees Washu from the reverse side of the ship (though they're unable to get back). Neutralizing the threat, Kagato mentally prods Ayeka before trying to take her blood into himself to learn the secret by force, but finds he is blocked from doing so by the very object of his pursuit - Tsunami, First Ship of Planet Jurai, patron of the Royal Family, and future incarnation of Sasami. Washu is able to free her daughter from her side of the ship in the meantime, but Ryoko is unable to fight to her full potential due in part to Ayeka's presence. What everyone did not know at the time was that Tenchi had survived the first attack, although the lower half of his body was destroyed by the blast. The remaining upper half was preserved by a branch of Ryu-Oh and the guardians Azaka and Kamidake until Tsunami arrived. Once aboard her ship, Tsunami was able to fully regenerate Tenchi's body and revived him. She then informed him about the battle with Kagato, for which Tenchi wanted to help. Tsunami agreed, but she also told him she could not accompany him… mostly because she didn't want to endanger Sasami as well.
Talking face to face again to his mentor after so many millennia, Kagato decides to show Washu a few new tricks. He draws in power from both Ryoko and her gems and the large scale ones he'd crafted aboard Sōja, meaning to cause the destruction of Earth as an experiment to reminisce about the old days. Tsunami again steps in to stop the blast as Kagato has anticipated, though he doesn't count on the shot being being reflected back at Sōja in bursts, bypassing the ship's shields. Kagato then plots to kill Ryoko on the spot so the full power of her gems will be Sōja's to use.
Tenchi is able to save Ryoko by severing Kagato's arm, though after the initial surprise the young man is beset, with Kagato taking the time to toy with him before invoking the power of the gathered gems into himself. As he draws Tsunami into his ship, Tenchi is despondent over his failure to save everyone, until he is reminded by a past talk with Tsunami to rely not on the sword, but on himself. Thinking him not quite sane, Kagato fires a shot at him directly, and is aghast to find Tenchi not only very much alive when the smoke clears but having produced Light Hawk Wings of his own - the only non-ship entity able to do so. Kagato is initially surprised, as the power from Tsunami that allows Light Hawk Wings to be created has been cut off from the rest of the universe, but he quickly realizes that these Wings come from within Tenchi himself and do not rely on any connection to Tsunami.
As Tenchi is able to ward off all projectile attacks, Kagato engages Tenchi point blank, and their dueling sword strokes hew each other in half. But while Tenchi is able to easily regenerate, Kagato finds he can not. He maintains his composure in his last moments, intrigued for the last time on how superbly done it all was. With Sōja cut in half as well, Tenchi and the others scramble to escape before it explodes.