Answering a distress call, the U.S.S. Voyager crew finds the Federation Starship Equinox, a vessel made for planetary research. Captain Ransom pleads with Janeway to extend Voyager's shields over his ship, which is under attack. As the shields are put in place, interspatial fissures erupt on several decks. Once a rescue team boards Equinox, they find many crewmembers dead of a thermolitic reaction. A few people are still alive, including Ransom, who explains that his ship was also pulled into the Delta Quadrant by the Caretaker.
Hostile aliens — flying nucleogenic lifeforms from another realm — are trying to enter the two ships at every fissure point. At the current rate, Voyager will be under full attack in less than two days. However, the aliens cannot survive inside the ship's atmosphere, so the crew sets out to create a multiphasic forcefield to trap the nucleogenic lifeforms and show them they cannot afford to continue their assault. Meanwhile, Ransom and Burke secretly discuss that they must hide their research lab and warp core from the Voyager crew.
Once Seven of Nine determines how to create a security grid that will protect the ships, Janeway decides it will be in everyone's best interest to abandon the Equinox and concentrate all efforts on preserving Voyager. Ransom and his crew prepare to steal Voyager's field generator and leave them behind. When Seven and Tuvok discover the research lab aboard Equinox has been deliberately contaminated with radiation to keep them away from it, Janeway sends in the Doctor to investigate.
The Doctor finds organic matter — from the nucleogenic lifeforms — which has been converted into a crystalline compound. The compound can be used to enhance the Equinox's propulsion systems. When Janeway learns that Ransom and his crew were planning to kill as many of the creatures as it took to get home, she confines them to their quarters and sets out to make contact with the aliens. Meanwhile, the Doctor goes back to the Equinox research lab and summons their EMH, which looks exactly like him. The Equinox Doctor explains that he created the conversion technology after his ethical subroutines were deleted. Then, he disables Voyager's Doctor and steals his holo-emitter.
Once the evil Doctor frees his crew from confinement, they beam back to the Equinox. Seven, who was onboard trying to disable their converters, is knocked unconscious. Before the security grid can be put on-line, Ransom and his crew steal Voyager's field generator. As the Equinox is set on course for the Alpha Quadrant at warp speed, Voyager's shields go completely off-line, and the aliens attack Janeway and the crew through fissures on all decks ...