Team Plasma steals this Dragon Skull from Nacrene Museum after the player earns their Basic Badge. The player confronts the culprit, a Team Plasma Grunt at the far end of Pinwheel Forest, and retrieves the skull, and immediately returns it to Lenora. Because the player obtains and gives away the skull in the same cutscene, they are not able to view it in their Bag.
In Pokémon Adventures, instead of merely the skull, Team Plasma stole the entire Dragon Fossil in The Mystery of the Missing Fossil, along with several other artifacts from the Nacrene Museum. Black agreed to help find the thieves, and, during his pursuit of the stolen items, encountered Burgh, whom Lenora had also requested to help solve the case. The two soon found the Dragon Fossil at the outskirts of Pinwheel Forest, where it, to their surprise, then begun attacking them. Black soon figured out that the ones responsible for the theft were a group of Team Plasma Grunts and Gorm of the Seven Sages, and they were using Gorm's Cofagrigus to control the skeleton. With Burgh's help, Black was able to defeat Cofagrigus. Upon realizing that the skeleton wasn't related to the LegendaryPokémon they were after, Team Plasma retreated, allowing the Dragon Fossil and the other stolen artifacts to be safely returned to the Nacrene Museum.