Having just watched it today to make up for accidentally missing it before: I refuse to believe they didn't. Boning offscreen isn't the same thing as not boning! Kdrama taught me that! We were a little confused why Chakotay and Janeway give off such 'yes, we're definitely dating' energy in some of the S3 episodes but now we understand.
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TANKTOP JANEWAY IS DEVASTATINGLY ATTRACTIVE.