Voyager takes heavy damage and suffers two fatalities (unnamed crewmembers are reported dead) in the first wave of the alienâs attack. The Equinox, with the knowledge that Voyager is under attack, continues its course back to the Alpha Quadrant. While recovering from the first wave, it becomes clear that the EMH from the Equinox is still aboard Voyager. He attempts to blend in and starts to tend to the wounded. On the Equinox, the captain attempts to convince Seven of Nine to join his crew, but she is unwilling to join. They begin to treat Sevenâs injuries and find the Doctor in the medical bay, who is informed that he too is a captive. When the Equinox attempts to bring its enhanced warp drives online, they find the drive has been encoded. Following Sevenâs unwillingness to divulge the codes, the crew of the Equinox deletes the Doctorâs ethical subroutines so that he will probe Sevenâs mind for the answers.
Janeway attempts to convince the aliens that Voyager is not a threat, but the aliens either do not understand or do not care. Chakotay questions Janewayâs desire to hunt down the Equinox, and she announces that she will do whatever it takes to bring the captain of the Equinox to justice. The Equinox hides in a region of space in which it will be harder to find them. The Doctor, now a bona fide psychopath, begins to probe Sevenâs mind for the codes, but is going to destroy her mind in the process. The captain makes an impassioned plea for Seven to divulge the codes of her own volition, but she is again unwilling to do so.
Janeway begins her search for the Equinox and studies the captainâs biography to discern what his next course of action will be. They find the Equinox, and after taking out the away team, the EMH on Voyager warns his captain that Janeway has discovered them, and both sides prepare for battle. They do a fair amount of damage to each other before Voyager completely disables the Equinoxâs weaponry. They flee and Voyager follows, but must ultimately break off their pursuit. While the Equinox jumps to warp, Voyager must stop to make repairs. Janeway begins a somewhat questionable interrogation of the captured Equinox crewman. Chakotay objects and rescues the crewman â which deeply affects their relationship. Janeway temporarily relieves him of duty and continues in her efforts to find the Equinox via the aliens that initially introduced the Equinox to the nucleogenic lifeforms. When they are finally able to establish communication with the aliens, Janeway eventually convinces them to stop attacking Voyager if she will give them the Equinox â she agrees.
The Doctor continues in his dissection of Sevenâs brain, and the stress of killing begins to take its toll on the Equinoxâs captain. The captain decides that it is time to give themselves up, but his first officer sets a mutiny in motion and prepares to attack Voyager. The first officer contacts the EMH to sabotage Voyager from within. The now deposed captain contacts Voyager and transports most of the crew to Voyager. The Doctor comes back to Voyagerâs medical bay and deletes the rogue EMH and informs the Equinox that they will no longer have help. The Equinoxâs captain disables shields and the nucleogenic lifeforms move in for the kill. To protect Voyager from the Equinoxâs explosion, the captain pilots it alone to a safe distance. Janeway reinstates Chakotay to second in command and the Doctor confirms that no permanent damage was done to Seven, who harbors no ill will towards him. Seven comments she will help The Doctor to establish security codes to prevent deletion of his ethical sub-routines in the future. Janeway strips the rank of all the former members of Equinox, but integrates them into her crew, although with severe restrictions.