While travelling the Delta Quadrant, Voyager is contacted by Starfleet Command via an improved subspace radio amplifier. From Starfleet Headquarters in San Francisco, Earth, Admiral Hayes relays a video message to Captain Janeway informing her that Starfleet has launched a new programme to bring the ship back to the Alpha Quadrant, and that Starfleet has dispatched two vessels to meet with Voyager, scheduled for five or six years' time. Janeway and her officers construct a response, informing Starfleet of their crew status, casualties, accounts of first contacts, and records of Borg activities in the area. While constructing the response, Voyager receives a standard Starfleet communiquÃ©, advising on the medical condition of Lewis Zimmerman, the Federation's leading holography expert and inventor of the EMH. According to the message, Zimmerman is dying, and the Federation's leading doctors cannot save him.
The Doctor advises that due to his immense experience with all manner of medical situations during Voyager's unusual journey, he may have experience and skill greater than that of Earth-based doctors. The Doctor approaches Janeway, who grants him leave to visit Zimmerman. Using the enhanced subspace radio relay established by Starfleet, Voyager transmits the Doctor's programme back to the Alpha Quadrant, a journey of 30,000 light years. However, the radio frequency cannot handle all of the Doctor's files, and Seven of Nine is obliged to shut down most of the Doctor's non-essential personality traits for the duration of the trip.
The Doctor manifests in the Solar system, aboard an immense Federation space station orbiting Jupiter, where Zimmerman has spent the last four years developing new holographic technology. Accompanying Zimmerman are Reginald Barclay, recently assigned as a research assistant, and a holographic female servant. The Doctor attempts to communicate with Zimmerman, but the scientist, a cantankerous and obnoxious old man, refuses to even speak to the Doctor, who he considers an obsolete and primitive example of technology. Zimmerman explains that the Doctor's model, the Mark I, was considered unsuitable by Starfleet for medical purposes, and that all Mark I's have been reassigned to menial labour on board waste barges, scrubbing plasma pipes. As a consequence, and because Zimmerman's Mark IVs and the best actual doctors on Earth have been unable to cure Zimmerman, the scientist refuses to deal with the Doctor. The Doctor is unable to reason with Zimmerman, and as their similar personalities clash, the two engage in a heated argument and refuse to speak to each other any more.
Concerned for Zimmerman's health, Barclay suggests that a counsellor is needed to smooth relations between Zimmerman and the Doctor, and contacts the USS Enterprise, only seven light-years distant, on a survey mission. He asks Deanna Troi to come to the station, and she advises that she will have to ask special permission from Captain Picard. Picard agrees, and Troi arrives at the station. However, she too is unable to reason with either the Doctor or Zimmerman, and storms out of the room after insulting both of them.
While speaking to Zimmerman's holographic servant, Troi realises that the hologram is less advanced than the Doctor, and that Zimmerman nevertheless respects her opinions. Troi prompts the hologram to talk with Zimmerman, and as she does so, Troi and Barclay secretly fiddle with the Doctor's files, convincing him that his programming is failing and that only Zimmerman, his creator, can save him.
Realising that they both need each other, Zimmerman and the Doctor patch up their differences, and the Doctor learns that Zimmerman's hostility is mainly due to his injured pride, resulting from Starfleet's decision to assign his hundreds of Mark I Medical Holograms to menial labour. Zimmerman stabilises the Doctor's programming and begins making enhancements to his data files; additions which the Doctor strenuously opposes, explaining that he is happy the way he is. Zimmerman agrees to stop making additions and allows the Doctor to treat him, using an experimental cellular regeneration therapy he concocted on board Voyager. Zimmerman begins to make a full recovery, and thanks the Doctor for saving him, adding that he is immensely proud of the Doctor's accomplishments; the only Mark I still doing the task for which he was built, excelling at it, and having developed a true personality, in spite of Starfleet's petty criticisms. Troi returns to the Enterprise, satisfied with her diplomatic accomplishments; the Doctor is transmitted back to Voyager, and Zimmerman, recovering, returns to his holographic research.