When Voyager comes across a large debris field, the crew concludes that it's all that's left of the alien space station they were approaching. Finding a strange trail of plasma particles at the site, they set course to solve the mystery of what happened to the alien vessel.
In the meantime, in an effort to expand the horizons of his program, the Doctor creates a "perfect" holodeck family: a wife named Charlene, teenage son Jeffrey, and a 10-year-old daughter named Belle. After he invites Kes and Torres to dine with his "family," Torres offers to tweak the program to make it more realistic.
As Voyager follows the particle wake, a tornado-like phenomenon rips out of subspace and bears down on them. The ship comes through the anomaly relatively unscathed and Chakotay suggests that the next time an astral eddy appears, they capture some of its highly charged plasma particles. Back in the holodeck, the Doctor is not pleased with Torres' changes; his wife works, his daughter whines and his son hangs out with tough Klingon teens.
Paris suggests that taking a shuttle into the wake of an eddy might offer the best opportunity to capture the valuable plasma particles. When another one forms, Paris attempts the maneuver, only to be caught up in yet another eddy. The crew watches in horror as Paris disappears with the eye of the astral phenomenon.
The Doctor tries to talk things out with his rebellious son. The conversation turns into an argument that's interrupted when word arrives that Belle has been seriously injured in an accident. Realizing she's going to die, he abruptly ends the holodeck program.
Paris learns that he's trapped between space and subspace, in the spawning area of the eddies. The only way out is the way he came in, inside a space tornado. As a huge storm appears in regular space, Voyager manages to beam Paris aboard. In Sickbay, Paris convinces the Doctor to return to his program and face the pain that life sometimes delivers. The Doctor reactivates the program and allows himself to grieve and draw comfort from the new closeness the tragedy brings to the remaining members of his family.