Question: At the beginning of the film, the Russians steal the body of the alien from the warehouse. Later in the film, after Indiana Jones gets the skull from the body of the conquistador, he gets captured by the Russians. Spalko pulls the skull out of the alien body and sets it on the table to do the whole "look into the eyes" scene. After that scene, and they escape the camp, the group is carrying around the skull from the conquistador in order to return it to the temple. So, what happened to the skull they pulled from the alien's body? Did they steal the body to get the skull for the sole purpose of having someone stare into it to experience the mental stimulation? Did they just ditch it afterwards?
Big Game
Answer: Spalko never pulled any skull from the alien's body. The skull Spalko "tortures" Indy with is Orellana's.
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Answer: There is no definite answer in the movie, but it probably ended up in a remote research facility in Siberia. Or perhaps Hruschevs' private collection. They stole the skull from the warehouse because they thought it was important in finding the alien vessel.