In the IDW continuity, the dōjō is an as-yet unnamed building in Mutant Town, Manhattan.
History
In Teenage Mutant Ninja Turtles #104, during a trip to the O'Neil Farm, the newly-reunited Leonardo, Raphael, Donatello, Michelangelo and Jennika discussed ideas for the future. Jenny told the others what Splinter had taught her back when she once asked him, "What is Ninja?", recalling how he told her that ninja originally organized as a grassroots defense among the poor and downtrodden to defend people without power. She suggested to the other Turtles that they could return to Mutant Town and help defend those who can't defend themselves. Leo went further with the idea, suggesting that instead of defending people, they could set up a dōjō to teach people basic self-defense and martial arts classes, as well as cultural studies like kadō, calligraphy, and then ongyō-jutsu and disguise for more advanced students. Later, at Splinter's grave near the farm, the five Turtles resolved to set up a new ninja clan that anyone could become a part of: The Splinter Clan. Nearby, the secretly eavesdropping Oroku Saki also approved of the idea.
Back in Mutant Town, the Turtles selected a ruined abandoned building and went to work fixing it up with the help of friends. The building also provided a place for the young mutants Lita, Zink, Zanna and Mushroom to stay, as Lita had been homeless and the weasels had nowhere else to go after their father Old Hob had tried to sell them to Oroku Karai.