Seven of Nine programs Holodeck 2 to be a rustic cabin where she practices the piano to the steady beat of a metronome, with her hair down and her Borg implants gone. Later, she attends a simulation of B'Elanna Torres' baby shower, where she again appears fully human and interacts with holo-crewmembers more freely than usual. She even makes a toast to the new baby. Just then the real crew on the Bridge detects mysterious energy discharges ahead, and Seven gets called to Astrometrics. Captain Janeway, Tuvok and Tom Paris meet her there, but Seven cannot find the source of the discharges. Opting not to alter course, Janeway turns her attention to the actual baby shower the crew will surprise Torres with later that day. Janeway asks Seven to be there, but she makes an excuse not to.
Instead, Seven returns to the holodeck where she creates new quarters for herself, and a holo-Neelix gives her advice on how to decorate the empty space. A holo-Chakotay arrives with a housewarming gift, a Native American dreamcatcher. Seven invites him back the following night for dinner.
At Seven's weekly physical in Sickbay, the Doctor tells her that Tom and B'Elanna missed her at the baby shower. Noting that her shoulder implant is out of alignment and her electrolyte levels are down, the Doctor learns that Seven missed her regeneration cycle. She claims it was because she was conducting "research" that had something to do with her personal life, which surprises the Doctor. Just then Voyager is rocked by another energy discharge, which produces a shockwave that then hits the ship violently and damages its warp drive. In Astrometrics, Seven discovers the explosion came from a subspace warhead that destroyed an unmanned probe. Since warp drive is down until repairs are complete, Janeway asks Seven to find a way to detect the warheads before they emerge from subspace, to give the crew a few seconds' warning.
Later, Icheb comes to Astrometrics to relieve Seven, because the Doctor wants her to spend more time regenerating. But instead of going into her alcove, she takes a belated baby shower gift to Torres in Engineering, and tries awkwardly to engage in small-talk. Then she modifies her holodeck program to fully decorate her quarters and put herself in an alluring dress for her date with holo-Chakotay. They prepare dinner together, and the mood gets increasingly romantic until they kiss. Suddenly Seven is distracted by a shrill noise, but she ignores it as she embraces her new simulated boyfriend.
The next morning Seven has disturbing dreams where she sees herself as a drone and her metronome appears as Borg technology. She wakes up when the real Chakotay summons her, which is odd because she's next to the holo-Chakotay. She arrives in Astrometrics where Icheb has picked up a warning beacon revealing that Voyager has entered a munitions testing ground. Chakotay is concerned that Seven was late for her duty shift, but she denies being distracted.
Later Seven is back in Holodeck 2 playing the piano for holo-Chakotay to the beat of the metronome. He's impressed by her flawless technique, but then he stops the metronome and tells her to play with more feeling. She's frustrated and anxious at first, but gradually she's able to play more from the heart, without needing to be perfect. Just then three alien missiles emerge from subspace and destroy a target probe, sending out shockwaves that rock Voyager. The real Chakotay calls on Seven for her sensor calibrations, but she needs a moment to return to her station. While the ship shakes hard, Seven gives Paris coordinates for other warheads about to emerge, but they turn out to be wrong. She corrects herself, and Paris is able to re-orient the ship to withstand the next shockwave.
In her Ready Room, Janeway chides Seven for being late with her sensor calibrations and for being away from her post, and asks why she's logged so much time in Holodeck 2. Seven tells a direct lie — that she's been running a simulation to improve ship systems — and apologizes for dividing her time while the ship is on alert. Janeway accepts her story and her apology, and looks forward to seeing her simulations. Seven returns to Astrometrics, where Icheb detects a strange attitude from her. Admitting she's been negligent, Seven leaves again to go "correct an error."
In the holodeck, Seven activates the Chakotay simulation again to end her relationship with him. Holo-Chakotay argues that every time she moves closer to her emotions, she backs away again, afraid that embracing her humanity will make her weak. She argues back that the ship needs her, but then she hears the mysterious high-pitched noise again, this time piercing through her head. She summons Sickbay and faints. The Doctor arrives and finds her going into neural shock. Seven wakes up in Sickbay, where the Doctor reveals that her cortical node began to shut down, but he managed to stabilize it. He asks what she was doing before she collapsed. She admits that she's been conducting simulations to explore different aspects of her humanity, such as social activities and intimate relations. She reveals that since Unimatrix Zero was destroyed, she's been trying to re-create some of the experiences she had there and feel some of those emotions again. But she plans to delete her holodeck programs because her "personal life" has distracted her from performing her duties efficiently.
Torres succeeds in getting engines back on-line, and Voyager jumps to warp. But then a subspace warhead locks onto the warp signature and targets the ship. The missile neutralizes a spread of photon torpedoes and continues closing in. Seven scans the warhead's detonator in an attempt to disarm it, but is unable to. Then she believes she can extract the detonator by transporting it out, but only at very close range. With no time to spare, she accomplishes the transport and the missile breaks apart harmlessly.
Later, the Doctor approaches Seven with bad news: Her cortical node did not malfunction, but in fact was designed to shut down her higher brain functions when she achieves a certain level of emotional stimulation — not surprising for a Borg implant. The Doctor believes he can reconfigure the node so she can continue her simulations, but it would be a difficult and lengthy process. Seven declines the procedure, saying that she's experienced enough "humanity" for the time being and the "failsafe" device will ensure that she's no longer distracted. The next day Chakotay invites Seven to a get-together in the Mess Hall, but she turns him down. He suggests that a little more socializing might do her good.