After more than three years of being stranded in the Delta Quadrant, Seven of Nine uses the newly extended range of the starship Voyager's sensors to locate an unattended network of alien sensor stations. Patching into this, she is able to locate a Federation vessel in the far reaches of the Alpha Quadrant. Hoping to finally make contact with home, Voyager's crew attempts to send a message along the relay, but it is reflected back to them after degrading en route. Theorizing that a holographic signal would be stronger, and not degrade so quickly, they send the Doctor as a datastream.
The Doctor finds himself in the sickbay of the USS Prometheus, an experimental warship developed in secret by the Federation. He learns from a dying crewman that the Romulans had learned of the prototype's existence and captured it. Being pursued by the USS Bonchune, the Romulans initiate the first test of the new multi-vector assault mode, in which the Prometheus splits into three separate pieces to engage hostile ships.
Seeking assistance, the Doctor activates the ship's own EMH, a Mark II version of the program (portrayed by Andy Dick). The second EMH cites protocol for an EMH to deactivate when its vessel was taken over, but Voyager's doctor notes that as both ships are at stake, they do not have that luxury.
Using the pretense of an infection on board, the Doctor goes to the bridge in an effort to open the atmospheric filters to flood the ship with anesthetizing gas and knock the Romulans unconscious. The ruse fails, but when he is captured and interrogated, the Doctor keeps the Romulans stalled long enough for the EMH Mark II to fool the ship's computer into opening the filters, permitting the distribution of the gas. Unfortunately, just moments after they take control, the Prometheus is intercepted by three Romulan D'deridex-class warbirds.
Unfamiliar with the helm and weapons systems, the two EMH programs unsuccessfully attempt to fool the Romulans into leaving, before three more Starfleet vessels arrive to retake their ship. In the ensuing battle, all six other vessels target the Prometheus. The EMH Mark II stumbles upon the command to put the ship into multi-vector assault mode. The strength of the Prometheus is quickly demonstrated when it easily overpowers and destroys one of the Romulan warbirds. With that loss, the Romulans retreat, and a Starfleet security detail transports over to the Prometheus.
Meanwhile, Voyager's crew has learned that the sensor array was not abandoned, but is claimed by the Hirogen, who announce themselves and demand that Voyager disconnect at once. Janeway tries to negotiate, but the Hirogen officer is recalcitrant. Seven of Nine buys time to await the Doctor's return by stunning the officer with a feedback loop. After the battle with the Romulans, the Doctor gets through and materializes in sickbay. He has good news: he has updated Starfleet Headquarters on Voyager's situation. This is the first time Starfleet has heard from the vessel since it disappeared four years ago. Voyager has been removed from Starfleet's list of destroyed ships, and a message sent back: "You're no longer alone." Starfleet will be trying their best to help return Voyager home and will tell the crew's families that they're alive.