As nucleogenic lifeforms attack Voyager, Captain Janeway discovers that she can use a deflector pulse to reinforce the shields and force the creatures off her ship. These attacks are occurring because the aliens are angry with Captain Ransom and the crew of the U.S.S. Equinox, another Starfleet vessel stranded in the Delta Quadrant. Ransom and his crew have killed dozens of the lifeforms for their organic matter in order to enhance the Equinox's propulsion systems and get back to the Alpha Quadrant. Now the aliens are trying to destroy both Starfleet ships.
Ransom and his renegade crew have escaped from Voyager's brig and taken back the Equinox, leaving Voyager behind and effectively kidnapping Seven of Nine and the Doctor, who were on board. When Ransom attempts to engage the enhanced warp drive, the ship stalls. They learn that Seven has locked out the power relays with codes that only she knows. Ransom tries to coerce the codes out of her, but when she refuses to talk, Ransom deletes the Doctor's ethical subroutines in order to solicit his help. The hologram then sets out to extract the information from Seven's cortical implants, which will severely damage her brain.
While the Voyager doctor is on the Equinox, the Equinox doctor in on Voyager. When Voyager gets away from the aliens and catches up with Equinox, the Equinox doctor manages to send Ransom a coded message to warn him. Janeway fires several photon torpedoes, badly damaging the Equinox. Ransom knows he cannot win, so he retreats into warp, temporarily escaping from Voyager. During the battle, Janeway managed to beam three of Ransom's crew aboard her ship.
Janeway has one of Ransom's captured crewmembers tied up and put in the cargo bay, ordering him to reveal Ransom's tactical status. She's prepared to drop the shields around the room and allow the alien lifeforms to come in and kill him. He refuses to talk, so Janeway and Chakotay wait outside the cargo bay as a fissure begins forming in the cargo bay. When Chakotay realizes that Janeway isn't bluffing, he breaks into the room and fires his phaser at the fissure, collapsing it before an alien can pass through. Janeway is shocked at Chakotay's disobedience and relieves him of duty.
Voyager manages to contact the Ankari, the race who innocently introduced the nucleogenic creatures to the Equinox crew. When the Ankari come aboard and summon the aliens, Janeway tells them that she will lead them to Equinox. When Voyager catches up with Equinox again, Ransom's conscience gets the better of him and he tells his crew that he is willing to cooperate with Janeway. Ransom's crew is not prepared to surrender, and his first officer, Lt. Burke, has Ransom arrested and takes control of the ship. Voyager begins firing on Equinox again, giving Ransom time to escape to the transporter room. Ransom then contacts Janeway, telling her that he is surrendering and will help her beam the Equinox crew aboard her ship.
The nucleogenic lifeforms also begin to attack Equinox. They manage to kill Burke before Janeway can beam him to Voyager. The only person left on board Equinox is Captain Ransom. With the warp core about to breach, Ransom tells Janeway to get as far away as possible, then he navigates his ship to a safe distance, sacrificing himself as the Equinox explodes.
Janeway reinstates Chakotay and strips the remaining Equinox crew of rank. She orders them to serve as Voyager crewman and tells them that they will have to earn her trust.