The Doctor is proud of his new project. He's created a family for himself on the holodeck and is spending time with them to expand his potential. Having designed a wife named Charlene and two children, Jeffrey and Belle, the Doctor (now called "Kenneth" by Charlene) invites B'Elanna Torres and Kes and for dinner, to show them what an excellent husband and father he's turning out to be.
They are less than amused. The Doctor's new family is far too good to be true: Charlene is a charming and wholesome hostess and takes pleasure in making sure her husband's every need is attended to (since he works so very hard), teenage Jeffrey is already an accomplished research scientist, and 10-year-old Belle is an adorable and well-rounded young student and athlete. Kes is polite, but B'Elanna says it plainly: no real family is so perfect.
The Doctor accepts Torres's offer to redesign his family more realistically: Charlene is now a busy working woman, Jeffrey is rebellious and wants to be accepted by Klingons, and Belle has begun playing the dangerous game of Parrises Squares.
At first, the Doctor feels that Torres's changes were too extreme, but he stays with the program. Eventually he receives the message that every parent dreads: Belle has fallen and hit her head at Parrises Squares practice, causing a life-threatening injury — and there's nothing the doctors can do to save her.
The Doctor visits his daughter in the hospital. Overcome with emotion, he orders the program terminated. However, he is faced with the logic of his crewmates: real life can't be switched on and off at whim. Confronted with this simple fact, the Doctor returns to the holodeck and resumes the program, returning to Belle's bedside in a hospital. Belle asks an emotional "Am I going to die?" to which the Doctor, at first replies "you're too sick to get better", and when Belle asks again "am I going to die", the doctor simply replies "yes". As a grieving Charlene and a tamer brother Jeffrey all enter the room and share their last few words with Belle, the family is brought together in an emotional hug when Belle dies.
Meanwhile, in a parallel story line of the episode, USS Voyager reaches the rendezvous where it was scheduled to meet with the Vostigye; but there is only debris, sixty Vostigye scientists apparently having died. The cause is not clear. Ensign Kim notes a strange subspace signal leading away from the station, so Captain Janeway decides to follow it. The Voyager crew finds no starships or life signs, but there is an increasingly large subspace disruption. A massive energy wave anomaly emerges from subspace as Voyager attempts to back away, but suddenly the anomaly disappears. "I'm not afraid to say it", Commander Chakotay says. "I've never seen anything like that before."
Janeway decides to investigate the anomaly further. Chakotay informs her that according to his readings it was an astral eddy that formed at the confluence of space and subspace. They prepare to anticipate the next such occurrence.
Voyager launches a probe. When the probe hits the anomaly, the ship is shaken worse than before. Telemetry shows that the anomaly has an interior temperature of nine million Kelvin, exchanges matter between subspace and normal space, and has a perfectly calm eye in the center. Janeway and Torres talk about trying to transport some of the anomaly onto the ship, but it disappears, taking the probe with it. The probe is still transmitting, and Torres detects some sort of energy, neither in space nor subspace. They then discuss taking energy, not from the anomaly, but from its waste. Voyager would disrupt the plasma, so Tom Paris goes in by shuttle. Exploring the eddy, he encounters turbulence and is pulled inside. When the eddy disappears from normal space, so does the shuttle – with Paris.
Voyager manages to regain contact with the shuttle, which is in an "interfold layer between space and subspace". Paris and the bridge crew are able to conceive and execute a plan for Paris to ride the eddy back into normal space, where he can be rescued.