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“To Be Alone With You” is about making sacrifices for love. There’s a lot things that can be read into that sentiment–religion, forbidden love, etc.
Insofar as the song is about Jesus (to whom Sufjan refers many times in this song, e.g., the Room of Acts 1:12-14 , Jesus' celibacy, going up on a tree, i.e., the cross), this song implicitly asks the listener the following questions: 1) Do you really desire to be alone with Jesus, to meet Him?; and 2) What would you give up to meet Him (especially considering what He gave up)? Is it worth it?
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