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In the IDW continuity, Clan Hamato refers to the family of Hamato Yoshi with his wife Tang Shen and their four children, and by virtue of reincarnation, also of Splinter and the four Turtles Leonardo, Raphael, Raphael and Michelangelo who represent the reborn lives of Yoshi and his children respectively.

The term was first used in the Vengeance story arc as "Clan Hamato" faced off against the "Clan Foot" in a traditional combat ritual, the Gauntlet.

When Clan Hamato prevailed in the Gauntlet and Splinter accepted becoming new jōnin of the Foot Clan (of which Hamato Yoshi had originally been a member), and three of his four sons (minus Michelangelo) became Foot Clan chūnin, Clan Hamato effectively merged with the Foot Clan.

But after Splinter's brutal execution of the unarmed Darius Dun in the Chasing Phantoms arc, the three sons cut ties with the Foot Clan and rejoined Michelangelo. Splinter gave his consent to their departure, dubbing his four sons once again as "Clan Hamato," both as an immediate family and as an officially-recognized ninja clan with Leonardo as its jōnin. By the Desperate Measures arc, Leo had come to embrace "Clan Hamato" as their family's official title, though he and his brothers continued to function more as a family who happen to be ninja rather than as a formal ninja clan.

In the Invasion of the Triceratons arc, Splinter came to use the term "Clan Hamato" in a darker and more menacing fashion when the Turtles came to visit their father to explain their knowledge of the situation. Upon arrival at Foot headquarters, the Turtles were forced to go through the strictures of conference protocol between separate clans, with Splinter and Leonardo as two clan jōnin meeting in private before the other brothers as members of one clan could speak openly to their father as members of another clan; these steps made the four sons feel especially unwelcome. With Splinter unwilling to entertain a peaceful solution to the conflict, he ordered his sons confined under guard both so that they could be protected and also so they could not interfere with the Foot's war efforts. Raphael pointed out that Splinter was inconsistently trying to have it both ways, in treating his sons with icy detachment as members of the separate Clan Hamato, while still yanking the chain of filial piety in demanding their obedience to him as their father.

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