In the 2003 cartoon, Hamato Yoshi's background was once again thoroughly revised. He was no longer a former member of the Foot Clan. His new origins are described in the season 4 episode "A Tale of Master Yoshi".
Hamato Yoshi was an orphan, who, begged in the streets of Tokyo Japan with his best friend, Yukio Mashimi, in the 1960s. When Yoshi returned a 5-yen coin dropped by the Ancient One, he took them in for their honesty, raised them as his sons, and taught them Ninjutsu. The two boys grew up together in the same house, and learning the same arts. Unfortunately, they both fell in love with the same girl,Tang Shen, another orphan taken in by the Ancient One. Tang Shen loved Yoshi more. During this time, Tang Shen spared a rat that had sneaked into the house and kept him as a pet.
One night, Yoshi, Shen, and Mashimi observed a lone man being attacked by four ninjas. Yoshi and Mashimi decided to help the man and fought off the ninjas. The man they saved was actually none other than Utrom Mortu and the ninjas were members of the Foot Clan. Impressed by their skill and having been partially exposed when his robotic arm was sliced off in the battle, Mortu gave Yoshi and Mashimi the offer to become Guardians, which they both accepted, despite their master's objections.
As a Guardian, Yoshi was promoted time and again, while Mashimi never seemed to advance. Mashimi grew jealous as Yoshi surpassed him in every way, and in his anger, he murdered Tang Shen and betrayed the hiding place of the Utroms to the Utrom Shredder. However Yoshi and the Utroms managed to escape with their lives. When Yoshi returned to the Ancient One, he found his master cradling Tang Shen's body. In anger, despite counsel from his master, Yoshi stormed the Foot's citadel and slew Mashimi in single combat for his betrayal.
With their Tokyo base compromised, the Utrom set up a new base in New York under the name T.C.R.I.. Yoshi went with them, taking Shen's rat with him. He named the rat Splinter to remind him what he had done and what he had failed to do.
However, the Utrom Shredder eventually tracked Yoshi down and tried to force him to reveal the location of the Utroms. Yoshi resisted and was tortured and murdered for his defiance. Splinter escaped and fled to the sewers, where he mutated along with the Turtles. He then proceeded to teach them Ninjutsu, just as he had learned from Yoshi. Splinter had grown fond, very fond of Yoshi, and after his mutation named himself in his honor Hamato Splinter and brought Yoshi's ashes back to Japan to bury him there.
Yoshi, a former Battle Nexus champion, is seen in flashbacks of the history of the Battle Nexus. A statue of him is in the hall of champions of the Nexus, and next to him are statues of Splinter and Michelangelo, who won the following two tournaments. Before the Utroms departed Earth, they gave Splinter an orb that contained a hologram of Yoshi. On some occasions it is possible Splinter, to contact the spirit of his old master. That orb was destroyed by the Utrom Shredder's adoptive daughter, Karai, when she attacked the Turtles' lair in the episode "Scion of the Shredder".
It's revealed in The Lost Episodes of the series that Yoshi and the Ancient One had tried, in vain, to get the Ninja Tribunal's help in the fight against the Utrom Shredder, warning them that the alien may channel the evil one. They refused as he was not the 'true' Shredder even though the Utrom Shredder was growing in power. Due to their refusal to help, Splinter partially blamed the Ninja Tribunal for Yoshi's death.
In episode, "Fathers & Sons", Splinter had procured Yoshi's ashes after his passing and made great strides to bring himself and the then-young Turtles to Japan. Yoshi's ashes were then laid to rest next to Tang Shen.
In the "lost" season five's final episode "Enter the Dragons, Part 2", when the Tengu Shredder goes to attack Splinter, a spirit of Hamato Yoshi manifested from the Turtles' medallions. He snatches the Shredder's trident and then slashes him with it, causing precious energy to leak from his armor. When the Tengu Shredder was on the verge of defeat, Yoshi manifests himself through the Turtles' medallions again, summoned by the combined power of the Turtles' dragon avatars, which shatters them and then he slayed the demon by slicing him in half. After delivering the final blow against the Tengu Shredder, he exchanges a brief and moving greeting with Splinter before he disappears.
- "The Shredder Strikes, Part 1"
- "Secret Origins, Part 3"
- "The Big Brawl, Part 1"
- "The Christmas Aliens
- "Exodus, Part 1"
- "A Tale of Master Yoshi"
- "Demons and Dragons"
- "Legend of the Five Dragons"
- "Enter the Dragons, Part 2"