In the story, George Bowlegs was shot and killed by Dr. Reynolds.
In Chapter 19, Lt. Joe Leaphorn had hoped to find George Bowlegs in the Shalako house at the Zuni village. However, he soon became discouraged when he found no sign of the boy. In the dance room, the Shalako (the "courier between the gods and men") and the Koyemshi (children of the son and daughter of the Shiwanni, the Sun Father) were participating in a ceremonial dance.
In a stroke of luck, Leaphorn had glimpsed George Bowlegs in one of the galleries across the dance room. The boy was entranced by the dancers and didn't see Leaphorn. For his part, Leaphorn pushed through the crowd in order to reach the passageway connecting the two galleries of the house. As soon as he made his way through to the other side, however, George was nowhere to be found. Thinking that the boy had ventured outside, Leaphorn followed.
He was soon rewarded when he glimpsed who he thought was the boy, prowling an alleyway between the Shalako house and another Zuni house. The alleyway opened into an unlit plaza, and at this point, Leaphorn had great difficulty in discerning his surroundings. Because of the lack of light, he became a little disoriented as he tried to navigate his way around. Eventually, a gunshot punctuated the night, and he was able to run towards the deafening sound. Just inside the alley, Leaphorn found George Bowlegs, lying motionless on the ground. George had fallen over the prayer plume he was carrying when he died.
Strangely, George Bowlegs' killer had been pulled by someone or something into an empty building. Even though Leaphorn shone his flashlight down the alley, Dr. Reynolds, the killer, was nowhere to be found. Later, as he explained to Ted Isaacs (the anthropology graduate student), Ernesto Cata, George's friend, had given George some of the artifacts he had stolen from Professor Reynolds' truck.
Since Professor Reynolds needed to protect his reputation (he'd been tampering with the excavation sites by salting them, an unthinkable offense), he proceeded to kill first Ernesto and then George. When Ted Isaacs told Leaphorn to bring Reynolds to justice, Leaphorn answered that no one would ever find Dr. Reynolds, as he had already been dealt with, under the law "that takes precedence over the white man's penal code...Thou shalt not profane the sacred ways of Zuni."
Dr. Reynolds killed George Bowlegs. Reynolds was in turn killed by three unnamed Zunis because he had defiled their sacred traditions.
Reynolds was a reknowned researcher and anthropologist who was committing the very serious crime of planting artifacts at an archaological site to support one of his theories. Ernesto Cata, a young friend of Bowlegs, stole some evidence from Reynolds' truck without realizing its significance, and passed part of it on to Bowlegs. Reynolds killed Cata and Bowlegs to keep the evidence, which would incriminate him and ruin his reputation, from being exposed.