Back on Earth, Lieutenant Barclay becomes obsessed with making contact with Voyager. During his project to contact Voyager, Barclay becomes consumed with the holographic recreations of the Voyager crew. Barclay seeks advice from his old friend from the Enterprise-D, Counselor Troi, who helps him deal with his growing problem.

Barclay is standing alone on the re-creation of the Voyager bridge, until he is interrupted on the viewscreen by his boss, Commander Peter Harkins. Harkins reminds Barclay of his duty to finish the transmitter diagnostics, so Barclay immediately ends the program as the bridge disappears.

Barclay then suggests that the team try to use an approaching itinerant pulsar in order to make contact with Voyager. By directing a tachyon beam at the pulsar, Barclay believes that it will produce a surge powerful enough to create an artificial wormhole, thus establishing two-way communication with Voyager. However, Harkins tells Barclay that they need to instead be focusing their time on Admiral Paris' visit and briefing.

Later that night when everyone has gone home, Barclay decides to once again activate the hologrid. He enters the holo-mess hall and sits down to play cards with holo-Paris, holo-Chakotay and holo-Kim. Barclay is confident and relaxed among the holographic crew and he tells them that they are his best friends. The next day, Barclay finds himself in the holo-Sickbay where the holo-Doctor tells him that he is an invaluable member of the crew. Then in the holo-mess hall, Kim and Paris both want to hang out with him. Barclay responds by telling his holo-friends that there is plenty of him to go around.

Back in the research lab, Harkins is briefing Admiral Paris and the other Starfleet Officials on the last known position of Voyager. Against Harkins' wishes, Barclay interrupts and begins telling Admiral Paris about his wormhole theory. Harkins is so upset with Barclay that he sends him home for the rest of the day. However, instead of following orders, Barclay enters the holo-briefing room and asks his holo-friends for technological advice. Janeway offers Barclay a team to help him work out the details.

Then, Harkins enters the lab and discovers that Barclay has created holograms of the Voyager crew. Harkins suggests that Barclay needs counseling because he has struggled with holo-addiction in the past. In the meantime, Harkins decides to take Barclay off of the Voyager rescue project.

Defying orders, Barclay goes to Admiral Paris' office where he asks him for access to the lab for one more day. If he is wrong about his theory, Barclay promises to resign from his position. Admiral Paris only agrees to order an independent review of Barclay's findings. If others agree that his idea is valid, then he'll order Commander Harkins to pursue his claim.

Back at Barclay's apartment, Troi expresses concern for Barclay's anxiousness and paranoia. Barclay begs Troi to tell the Admiral that he is psychologically fit to return to work. Barclay admits that he has created a new family since he left the Enterprise, however, the family he has created is not real. Troi tells Barclay that she has requested a temporary leave of absence from the Enterprise so she can stay a while longer.

That night, Barclay once again defies order and heads to the research lab. His code is de-authorized, so he manipulates the computer to get inside. Once in the lab, Barclay accesses the MIDAS Array, directs a tachyon beam toward the pulsar to open a micro-wormhole, and sends a message to Voyager in hopes of getting a response. Suddenly, Harkins enters the lab and instructs Barclay to step away from the controls. Instead of following orders, Barclay tells the computer to transfer control to the hologrid.

Barclay tells holo-Tuvok that there are two security guards after him, and he orders the computer to trap them with a forcefield. While Harkins works on shutting down the program by simulating a warp core breach, Barclay continues to work on making contact with the real Voyager through the wormhole. Harkins and two other guards catch up with Barclay on the holo-Bridge, where holo-Janeway alerts the crew to the presence of intruders. Barclay immediately commands a forcefield, which prevents Harkins and the guards from reaching him, while he begs for more time. However, the holo-Voyager is about to self-destruct, so Barclay voluntarily ends the program and gives himself up.

Meanwhile on the real Voyager, Seven of Nine has detected an artificial micro-wormhole whose origin is in the Alpha Quadrant. Janeway immediately instructs Paris to lay in a course toward the range.

Back in the Pathfinder lab, just as Harkins asks Admiral Paris what he should do with Barclay, they receive a response from Voyager. Janeway and Admiral Paris are able to converse briefly and he tells her that they are doing everything in their power to bring Voyager back.

Harkins apologizes to Barclay for ever doubting him, and Admiral Paris announces the beginning of "Project Voyager." Meanwhile in the Delta Quadrant, the Voyager crew toasts Barclay, even though they don't personally know him, for his extraordinary efforts. Back on Earth, Troi congratulates Barclay, and he tells her about the woman he's started dating.