After successfully extending the range of Voyager`s sensors, Seven of Nine locates a network of alien sensor stations. Patching into this, she is able to locate a Federation vessel on the far reaches of the Alpha Quadrant, the USS Prometheus. 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.
Upon arrival, The Doctor discovers that the Prometheus is an experimental warship developed in secret by the Federation, however the Romulans have learned of its existence and captured the vessel. Being pursued by the USS Bonchune, the Romulans initiate the first test of the new multi-vector assault mode, in which Prometheus splits into three separate pieces to engage hostile ships.
Seeking assistance, The Doctor activates the ship's own EMH, a Mark II of the program. 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 were 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, by the time they take control, Prometheus has reached the designated rendezvous point, and three D'deridex-class warbirds are ready to take delivery. 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 Prometheus. 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, the Hirogen, owners of the sensor array, have contacted Voyager, and demand they log off the relay. Seven of Nine zaps the threatening Hirogen officer with a feedback loop, and the Voyager crew await a response from the Alpha Quadrant. After the battle with the Romulans, the Doctor gets through and materializes in sickbay. He has good news: he has updated Starfleet on Voyager's situation. This is the first time Starfleet has heard from the vessel since it disappeared four years ago. Voyager was removed from the Starfleet list of destroyed ships (having been listed for fourteen months), and a message sent back: "You're no longer alone". Starfleet will be trying their best to return Voyager home, as well as tell their families that the crew is alive.