When Seven of Nine locates an alien relay station, she establishes a sensor link and detects a Starfleet vessel in the Alpha Quadrant. Janeway uses the relay network to send a message to the ship, but the transmission degrades before it gets through. Their only other option is to send a holographic datastream. The Doctor is recruited, and he finds himself aboard the U.S.S. Prometheus, only to find that the Starfleet crew is dead and the ship is in Romulan hands. Prometheus is a prototype with advanced tactical abilities that the Romulans are eager to test. They access the ship's multi-vector assault mode and the vessel splits into three separate ships. Moving into attack formation, they easily destroy a Starfleet vessel, then reintegrate.
The Doctor activates the Prometheus' Emergency Medical Hologram (EMH-2), and the two agree to work together to stop the Romulans. They plan to use the ventilation system to distribute an anesthetic gas, but the Doctor must first reach the environmental controls on the Bridge. He concocts a story about a virus to gain access to the controls, but the Romulans are suspicious.
Meanwhile, Voyager's link to the relay station is severed by the Hirogen, the species claiming ownership of the communications network. Seven sends a mild shock to the Hirogen, giving them a bit more time.
As the Doctor is grilled by the Romulans, gas suddenly pours from the vents, incapacitating the enemy. EMH-2 explains that he simulated a bio-hazard, and the computer opened the ventilation system automatically. Now the doctors are faced with flying the ship, which is headed into Romulan space. The Prometheus is fired upon by enemy warbirds, but the doctors can't figure out the controls. Then they're fired upon by Starfleet ships, who think Romulans are still in command. At last EMH-2 accidentally initiates the decoupling sequence, and the doctors score a direct hit against a Romulan ship, causing the other warbirds to retreat. Starfleet personnel beam aboard, and after speaking directly with Headquarters, the Doctor is transmitted back to Voyager, where he conveys a message: Starfleet Headquarters is now aware of their predicament, and will do everything it can to bring Voyager safely home.