In the Post-World War II era, when Japan was still recovering from its defeat, it was not uncommon to see young orphans begging in the streets. Hamato Yoshi and Yukio Mashimi found a coin that the Ancient One dropped. Mashimi wanted to spend it but Yoshi gave the coin back. The Ancient One, pleased with the boy's kindness, offered to give it back if they could swipe it from his hand; the former failed but the latter succeeded. He took the two boys into his home, where he trained them in the ways of ninjutsu like his own sons. He also adopted another orphan girl Tang Shen, with whom both of the boys fell in love with. However, she only had feelings for Yoshi. When the boys became men, they saved Mortu from the Foot Clan when they discovered his Utrom nature, he offered them the chance to become Guardians. The Ancient One forbade them because he sees they need mental training. But as men, they made their decision and became Guardians. The Ancient One went with Yoshi to ask the Ninja Tribunal to ally with the Utroms against the Utrom Shredder impostor but the latter refused as he was not the true Shredder, ignoring the possibility that Ch'rell could challenge his namesake.
Unfortunately, the Ancient One failed to see that Mashimi became angered at his lack of success as a Guardian and losing Tang Shen to Yoshi. He killed the latter and revealed the Utroms' location to the Utrom Shredder. Yoshi was furious at this betrayal, but Ancient One cautioned him that hate can spread like a splinter. Mashimi killed Tang Shen, and in return, Yoshi killed Mashimi. When Yoshi killed him, he left Japan to go to New York, naming his rat Splinter to remind him of these past events.
Years later, the Ancient One would encounter Splinter once again, in a more evolved humanoid form. The Ancient One was surprised, assuming him to be a demon until he learned who he truly was. He couldn't accept that Yoshi was dead. He went to the Lap of the Gods to tell the Tribunal of Yoshi's loss; they already knew, but were unconcerned. But unknown to him, he had led a bone demon to the sanctuary, guided by the Foot Mystics to locate the original Shredder's remains. But as Splinter's young turtle sons could see him, broke the necklace that made him concealed to all but the young and pure. The Ancient One and Splinter defeated the demon. The Tribunal then erased the young ones' mind of the recent events to protect them. Before departing, the Ancient One gave the young turtles ninja masks.
Years later, the Ancient One patiently awaited Leonardo's arrival to guide him to the right path, for the young turtle blamed himself for letting his family get hurt at the hands of the Utrom Shredder and became more aggressive and cold. The Ancient One didn't reveal his identity to the turtle in the journey to his other home. He calmly told Leonardo to let ghost demons defeat him. At his temple, he showed Leonardo's greatest enemy — himself. Leo comes to the revelation that the Ancient One was right beside him the whole time. He took Leo under his tutelage, teaching him wisdom and greater skills. But while meditating, the Ancient One had a premonition of the new Shredder, Karai and told Leo to go back and save his family.
A little while later, The Ancient One went to the Tribunal (who ironically refer to him as "Young One") to plead them not to choose the Turtles as Acolyes but he was too late, as they made their decision. He went to New York to try to stop them from being captured but was late again. Reluctantly, he guided Splinter to the Lap of the Gods, where they supervised the Turtles' training as acolytes.
The Ancient One returned to New York with the Turtles and Splinter when the Foot Mystics defeated the Tribunal and retrieved the Shredder's remains and came to the city to revive the evil one there, where he would revenge himself upon Karai.
When the Shredder was defeated, the Ancient One was summoned by the Tribunal to "move on", which he humbly accepted.