Only #3 is possible. #1 would be possible this way: He made friends with her. #2 would be possible this way: He had a friend in her.
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RinoThen, what does "to have a friend in someone" mean?It simply means that the 'someone' is a friend. The theme song of Toy Story: http://prezi.com/jrejra9ilh_j/toy-story-theme-song/
RinoIt sounds to me that "in" emphasizes there is a more spiritual relationship or a deeper bond instead of a shallow relationship between people.I don't see that at all, sorry.