The trivia item below may give away important plot points.
In an interview, Michael Shanks revealed there was an alternate ending shot for the film. Following Landry telling him that the Ark being stored in Area 51 is out of his hands, Daniel meets with the team. He convinces them that it is too dangerous to be left in the government's hands and they agree. They then plan and execute a raid on the facility and take back the Ark. Shanks said he isn't quite sure why it was cut other than the fact that maybe the movie had "too many endings".