Some TMNT stuff really isn't for little kids.
In the IDW continuity, the Natural History Museum is located in New York City. It appears both at the beginning and at the end of the mini-series TMNT: Bebop & Rocksteady Destroy Everything!, where the Turtles visit an exhibit called "The Mysteries of the Ancient Sorceress," whose centerpieces are the mummified body of a future version of Renet and the complete skeletons of Bebop and Rocksteady, all dated to the Cretaceous period of Earth's remote prehistory.
In issue #1, Michelangelo touches a gem on the mummy's body, and an automated reaction summons the younger Renet to their location, and she reveals that the gem is actually a Stasis Beacon that was meant to teleport her to that time and place when the Turtles touched it. Renet is equally confused about why the exhibit also has skeletons of Bebop and Rocksteady, but Renet is also aware that the fossils are from the same time period that Savanti Romero was banished to (in the Mirage continuity), so she and the Turtles travel back to the Cretaceous to investigate, kicking off the miniseries' events.
In issue #5, it has been established that Bebop and Rocksteady from the IDW continuity did indeed time travel back to the Cretaceous and teamed up with Savanti Romero, but that it was not their bones that fossilized over millions of years and made their way to the exhibit, but those of their 1987 TV series versions. And the mummy of future Renet in the exhibit was not dead, but just preserved in stasis; when younger Renet removed the gem from the mummy, the future Renet came back to life. However, with her revival, the exhibit had lost its centerpiece.
The museum reappears in Teenage Mutant Ninja Turtles issue 85, when Leatherhead visits during closing hours. His presence is noticed when April O'Neil discovers he has destroyed one of the Mousers; she notifies the Turtles who promptly pay him a visit. Leatherhead has knocked a security guard unconscious, but the only injuries sustained were his own from when he destroyed the Mouser. He and the Turtles talk peacefully for a short time, until Leatherhead starts hallucinating the deceased Krang taunting him (Leatherhead having been the one who killed him). Leatherhead becomes violent towards the nonexistent Krang and the Turtles try to contain him, with their scuffle damaging some exhibits and collapsing a dinosaur display skeleton. Leatherhead soon runs shouting out of the museum on his own, and it is clear to the Turtles that Leatherhead is still dealing with severe psychological trauma.
- Though apparently a fictionalization of the American Museum of Natural History, this version of the museum is never referred to by that name, and even the museum exhibit's hanging poster uses branding that refers to the "Natural History Museum" rather than the "American Museum of Natural History."