The crew encounters a protostar and Captain Janeway decides to have samples beamed aboard for use as a potential power source. A problem occurs when beaming the samples to Voyager.
Janeway recommends to BâElanna that she should have Ensign Kim's assistance, but it turns out that he is missing. The crew finds his holodeck program Beowulf still running. With each person sent into the holodeck also becoming lost, Captain Janeway finally sends in The Doctor to investigate, under the assumption that, as an already immaterial hologram, he could not be dematerialized the way the missing crew had been. As The Doctor shows signs of nervousness when preparing for this, his first "away" mission from sickbay, so Kes encourages him to take a name to embolden him with having an identity of his own. He takes the name of "Schweitzer" from a selection of three. The other two were never given.
Once into the holodeck, "Schweitzer" meets Freya, a Shieldmaiden. After taking him to the hall, where he is made to prove himself before the others, and after a celebratory meal, after which everyone has retired to separate rooms, she reappears and suggests that in the cold of the night when the fire in his hearth has gone out that he ought to join her. But he reluctantly dismisses her advances; he overcomes this reluctance in later episodes. Later they are confronted by an attacker and Freya is killed, dying in "Schweitzer's" arms. With her last words she hauntingly speaks his name.
As The Doctor investigates further, he realizes that within the containment field into which the protostar samples were transported that alien energy lifeforms were also beamed into the ship but one managed to escape through a breach during the process. It escaped to the holodeck and began converting the matter of every person who entered into energy. Once the energy samples holding the other lifeforms are returned to the alien in the holodeck by The Doctor, in kind, the missing crew are returned to their original forms.
Afterwards, upon reflection, The Doctor decides not to keep the name Schweitzer, as his memories associated with it are too painful. He remains unnamed throughout the rest of the series with notable exceptions in the episodes "Before and After", "Endgame" and "Lifesigns", though other people attempt to give him names.