The Equinox takes off after having taken kidnapped Seven of Nine and the Doctor, leaving Voyager left to fight the interspatial aliens. Voyager then purses the Equinox, and is aided by subterfuge by Seven. However, The Equinox’ Captain removes the Doctor’s ethical subroutines and the Doctor tortures Seven to recover codes she has refused to give up.
Meanwhile, on Voyager the EMH from the Equinox, who also has had his ethical subroutines removed, has replaced Voyager’s EMH, and is attempting to hinder Voyager’s attempt to overtake and capture the Equinox.
Can Voyager overcome the EMH’s deceptions and some of the duplicitous crew of Equinox crew who were previously beamed aboard? It appears the answer lies with contact with the interspatial aliens.