The American Museum of Natural History, located at 79th Street and Central Park West, is one of the largest and most celebrated museums in the world. Over the years it has been the site of many superhuman battles, with large parts of the museum being repeatedly demolished and rebuilt.
Stegron infiltrated the museum and used a stolen "retro-generation ray" that transformed the museum's skeletons back into living, flesh-covered dinosaurs, which he intended to use as his personal army. Spider-Man was able to stop him and the dinosaurs reverted back into skeletons. 
At the behest of archaeologist Gladstone Hawkins, the special S.H.I.E.L.D. detachment known as the "Godzilla Squad" lured a then twenty-foot Godzilla into the Museum of Natural History where they had hoped to trap it. Their plan nearly worked and they succeeded in keeping Godzilla somewhat serene, until the arrival of the Fantastic Four. The Thing, always itching for a fight, provoked Godzilla and the two battled one another destroying many of the museum's exhibits.
The criminal Batroc and his Brigade broke into the Museum to steal the bones of Ulysses Bloodstone, to deliver them to his employer, Baron Zemo.
Stegron later launched a second attack from the museum, this time using the powers of a mysterious asteroid to amplify the bestial aggression of everyone in the city, especially those with animal-based powers. Large portions of the museum were once again destroyed.
Archaeologist Jaime Slade received a delivery of southwestern Indian artifacts for a special exhibition in the Museum; the shipment was damaged when Hawkeye and Mockingbird fought a gang of arms dealers directly in front of the museum. Sifting through the damaged truck, Jaime retrieved a special urn, containing the ashes of her ancestor Lincoln Slade, the villainous Old West Phantom Rider who had drugged and assaulted the time-travelling Mockingbird in 1876. Jaime was immediately possessed by the spirit of Slade, transforming her into the latest incarnation of the Phantom Rider. Later, Hawkeye and Mockingbird laid a trap inside the museum for the Phantom Rider and her ally Crossfire, who had teamed up with her to kill the two heroes. Crossfire and Phantom Rider blew a large portion of the museum's roof off, and sent a wave of attack drones inside to kill the heroes. Mockingbird obtained the urn from within the museum and teleported the entire group to Nevada in the hopes of exorcising Lincoln's spirit from Jaime's body.
Batroc once again broke into the Museum, this time to steal a precious diamond. He ended up fighting Fantomex who had come for the same reason.
- 52 Appearances of American Museum of Natural History
- 2 Minor Appearances of American Museum of Natural History
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