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Reginald Barclay and Admiral Paris from the Pathfinder project on Earth appear on the Astrometrics domescreen and tell Captain Janeway that the com link will only work for only 11 minutes a day. Three people can talk to their loved ones in the Alpha Quadrant for three minutes per day, so Neelix has the crew draw numbered isolinear chips. The Doctor draws number one, so he contacts a well-known Bolian publisher on Earth — Ardon Broht of Broht & Forrester — to discuss the holonovel which he had previously transmitted to him. Broht raves about the piece and wants to distribute it right away, but the Doctor insists on making revisions first. Later, the Doctor brags to Lt. Tom Paris about his conversation with the publisher, which raises Paris' curiosity about the hologram's opus. He convinces the Doctor to let him experience the holonovel, which he learns is titled "Photons Be Free."

Paris finds himself in the role of the Emergency Medical Hologram (EMH) aboard the "Starship Vortex," and he sees that the first chapter starts out almost identically to the Doctor's own experience of being first activated. The other characters resemble the real crew, but altered slightly in their appearance — for instance, Chakotay is a Bajoran. When Paris, as the Doctor, decides to treat a critical patient ahead of a bridge officer, Captain "Jenkins" (Janeway with black hair) enters Sickbay and kills the dying crewman, so that the bridge officer can now be treated. Shocked at how the crew is portrayed, Paris tells B'Elanna Torres and Harry Kim about it, and they think he's overreacting. So Paris tells his crewmates to try it out themselves.

Torres experiences for herself how badly the "Vortex" EMH gets treated by the holo-crew, especially her own look-alike; Neelix, in the same role, is scolded and threatened by Captain Jenkins; and Kim becomes part of an escape plan with help from "Three of Eight." Finally, Janeway experiences the final chapter of the holonovel, where the EMH is brutally decompiled. She immediately orders the Doctor to report to her Ready Room.

The Doctor defends the piece, claiming it's a work of fiction with an important message. Janeway wonders if the Doctor sees himself as oppressed, but he explains he intended to draw attention to the plight of his "brothers" in the Alpha Quadrant, other EMH Mark Ones like him who have been condemned to menial tasks. Janeway asks him to consider how his writing makes his friends feel, but he won't compromise on his self-expression. When he returns to the holodeck to make final revisions, he finds the program altered with a holo-Paris as the narrator, and the story about the assistant to the Chief Medical Officer who has to learn to tolerate his overbearing manner and obnoxious behavior. Incensed, the Doctor confronts Paris about distorting his work. Paris assures him he kept the original intact, but was simply trying to make a point that someone running a program like that would think the characters were based on the real people. But what bothers Paris most is that the immature, self-indulgent character that bears his likeness apparently reveals what the Doctor really thinks of him.

Neelix talks to the Doctor and helps him realize that by publishing his program, he may hurt the people he cares about, and he can make adjustments so that it's not so obviously based on Voyager without sacrificing his theme. But a rewrite will take weeks and the publisher is expecting a final draft tomorrow. Neelix tells the Doctor to give the publisher a call, and hands him his numbered chip. Broht is not happy to hear that the work will be delayed, but the crew is grateful to the Doctor for taking their feelings into account, and Paris agrees to assist with the revisions.

Meanwhile, members of the crew get to talk to family members they haven't seen in years. Kim's parents wonder when he's getting a promotion, and offer to write Captain Janeway a letter, which Harry strongly discourages. Torres begrudgingly agrees to talk to her father, who abandoned her when she was a child; during their awkward conversation, John Torres expresses regret and hopes they can get to know each other again. Even Seven of Nine uses her com time to contact her nearest living relative, an aunt on Earth; Irene Hansen tells Seven about how she was as a child, and calls her Annika.

Janeway receives an urgent message from Admiral Paris: He just learned from Barclay that the Doctor's holo-novel has been distributed and is being played in thousands of holosuites. The Doctor contacts Broht demanding a recall and a public apology, but Broht refuses. Janeway points out that authors have rights, but Broht responds that under Federation law, holograms have no rights.

After discussing legal options with Tuvok, Janeway decides to request a hearing to seek the same rights for the Doctor as any flesh-and-blood person. A Federation Arbitrator hears arguments from Broht and from the Voyager crew, who testify that the Doctor has demonstrated the traits of a "person" such as creativity, ambition, friendship and fallibility. After several days of arguments and deliberations, the Arbitrator announces he is not prepared to rule that the Doctor is a "person" under the law, but he is willing to extend the definition of "artist" to include the Doctor; therefore he orders all copies of the holo-novel recalled immediately. The Doctor apologizes to Janeway for the damage that's been done, but the crew encourages him to continue revising his work and to find a new publisher. Four months later, on an asteroid in the Alpha Quadrant where hundreds of EMH Mark Ones (all identical to the Doctor) are now mining dilithium, word gets around among the holograms that there is a very provocative new program in the holo-lab called "Photons Be Free."

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