Bailey was trapped inside the Great Rotunda with D'Agosta and others after the power failure brought the security doors down. He helped D'Agosta lead a group of guests including Mayor Harper through the subbasement in hopes of finding an exit to the museum. While descending a staircase, Bailey and museum security director Ippolito were at the rear of the group when Mbwun attacked. Ippolito was mauled and killed. Bailey, though covered in Ippolito's blood and flesh, was unhurt.
Bailey and D'Agosta remained in radio contact with the FBI as they moved through the subbasement. Special Agent Spencer Coffey attempted to relieve D'Agosta of duty and put Bailey in charge, hoping that he would lead the group back upstairs to the Rotunda. Coffey did not believe D'Agosta's report that there was a murderous creature loose in the building. Bailey confirmed D'Agosta's story and silenced his radio, infuriating Coffey.
As the group moved deeper into the basement, Mbwun returned. Bailey turned and fired two shots from his shotgun at the beast allowing the others to run ahead. He continued to cover the rear of the group. When Mbwun returned a third time, Bailey turned to face it. He fired his shotgun but was quickly cut down. D'Agosta heard the crunching noise of Mbwun chewing on his body.
In the aftermath of the Museum Beast Murders, journalist Bill Smithback declared that half the royalties from his upcoming book would be donated to the Officer John Bailey Memorial Fund, to benefit his family.