The deltaflyer is boarded by an alien race, and to avoid for the Doctor's program to be confiscated, Seven intergrades his system, with her neuronaptical Borg implants (or however it's all spelled). So, to make a long story short; the Doctor now has complete controle of Seven's body, however her body has also complete controle of the Doctor, meaning that if the body feels pain,so does the Doctor. Along with other physical emotions!

From "Star Trek: Voyager", Season 7, Episode 7 "Body and Soul"
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