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The theme of the story is the story's main message or lesson about life. The lesson is usually the lesson that the main character learns.
What do you think Carl Sagan was trying to say about technology and religion (faith)? (Think about what Ellie learns.)
Ellie learns that some things in life cannot be proven by science. She learns to acknowledge something bigger than herself and science, something that cannot be explained but which she knows in her heart is true and real.
Sagan isn't saying technology is bad, but it can't keep people from being lonely either.