B'Elanna Torres starts the morning in an uncommonly good mood, but then in Engineering her mood changes and she scolds Icheb for being there without her permission. Suddenly she gets dizzy and drops to the floor. Seven of Nine goes to help as Icheb scans her with a tricorder. Icheb says he detects a lifesign inside Torres, perhaps a parasite. But Seven contacts the Doctor and tells him Torres may be pregnant. In Sickbay the Doctor confirms to Torres and her husband Tom Paris that they are indeed having a baby, and the reason Torres fainted could be that Klingon and human metabolism sometimes clash. The fetus is healthy, but the Doctor warns Torres that she can expect to experience some behavioral volatility.

Despite Tom and B'Elanna's wish to keep the news to themselves for awhile, the rest of the crew quickly finds out about Torres' pregnancy, and both Neelix and Chakotay vie to be the child's godfather. Captain Janeway offers Torres time off, but Torres insists that she can handle her duties. Meanwhile an increasingly anxious Paris faces the prospect of being of father, and even solicits advice from Tuvok. Later Paris has a candlelight dinner set out when Torres returns to their quarters, but she's upset about the Captain practically relieving her of duty and annoyed by crewmembers' unsolicited advice. She gets further upset when Tom makes a comment about her being a Klingon mother. B'Elanna catches herself in "behavioral volatility" and calms down, but then the Doctor summons them to Sickbay.

Tom and B'Elanna learn their child's spine will be deviated, but that a genetic modification will correct it. The Doctor also accidentally reveals that it's a girl. At Tom's request, the Doctor projects an holographic image of the baby. Tom thinks she's beautiful, but B'Elanna wonders why the girl has forehead ridges when she's only one-quarter Klingon. The Doctor says Klingon traits remain dominant for several generations. B'Elanna has a flashback to a time when she was a young girl on a campout with her human father, and recalls that he told her how much she was like her Klingon mother. Later, Paris and Torres turn in for the night, and Torres continues to recall the campout experience from when she was 12-years old. Young B'Elanna didn't want to go hiking with her human cousins because she thought they didn't like her.

The next morning Torres reports to Sickbay to undergo the Doctor's recommended genetic treatment. While lying on the bio-bed she has another flashback from the campout: one of her cousins, an 11-year-old boy, put a worm in her food and teased her about being Klingon, causing young B'Elanna to storm off. After the Doctor completes the treatment successfully, Torres goes to a holodeck and projects a computer-generated image of her daughter when she will be 12 years old. Seeing her forehead ridges, Torres examines the child's genetic makeup, and deletes certain gene sequences in the computer display. Asking the computer to extrapolate the genetic changes to the projection, she eventually causes the girl to look completely human. Torres saves the changes and restricts access to the file for herself.

Torres returns to Sickbay and tries to convince the Doctor to make further genetic changes in her baby, claiming it will prevent potential health problems. The Doctor is against the idea and suggests that she talk this over with Paris. When she does, Paris is totally against the idea. He comes to realize the issue is not about the child's health, but the fact that the child is part Klingon. He tries to assure her that their daughter will not be treated like an outcast. But they fail to come to an agreement, and turn to Captain Janeway. Torres argues that she wants to make physiological changes for her child's best interest, just as Janeway did for Seven of Nine. Janeway points out their problem is not ethical, but marital, and she would not overrule the Doctor. Torres is not happy that Paris has gotten his way, and before he knows it he's at Harry Kim's doorstep needing a place to sleep.

Torres sits in bed alone, recalling more of the campout experience. Young B'Elanna finally returned to the campsite after having run off, and told her father, John Torres, that she wished she wasn't Klingon because everyone made fun of her and her schoolmates hated her. Despite her father's assurances that the other kids didn't hate her, young B'Elanna chose to sit alone and read rather than join the rest of her family around the campfire. In the present moment, Torres re-experiences the isolation she felt back then.

While working in Engineering the next day, Torres recalls when she overheard her father talking to Uncle Carl about how moody and argumentative young B'Elanna had become, just like her mother. John reminded his brother about their parents' reservations about him marrying a Klingon, and noted that now, ironically, he was living with two of them. Later Torres meets up with Paris in the corridor, and they reconcile. They are then summoned to Sickbay.

The Doctor tells Torres and Paris that he reviewed the data and has concluded the genetic alterations she wanted are necessary because the "clash" between Klingon and human metabolism is more extensive than he realized. The child risks complete metabolic failure, and to prevent it he must eliminate most of her Klingon genetic material. The Doctor schedules a procedure for the next morning. Meanwhile a disturbed Paris takes the Doctor's findings and runs it by Icheb, who spots a computational error. Seven runs a diagnostic on the Doctor and discovers that his program has been tampered with. Paris tries to contact Torres, but she doesn't respond. The computer reveals she's in Sickbay. Torres has already arranged to undergo the procedure to alter the baby.

Torres has blocked communications to Sickbay and access to the Doctor's program, so Paris, realizing that Torres manipulated the Doctor to "change his mind," summons Tuvok to meet him at Sickbay. They have to manually open the door, and then encounter a forcefield. Paris orders the Doctor to stop the procedure, but Torres tells the Doctor to ignore him. Eventually the forcefield is cut off and Tuvok informs the Doctor he's been altered, so he agrees to deactivate himself. Tuvok leaves Paris and Torres alone. The couple argue over Torres' actions, and in the heat of the moment Torres reveals her issue is with her father. She tells Tom about how she and her father grew apart, and during the campout when she was 12, she blurted out to her father that if he can't stand living with two Klingons, why doesn't he just leave. And several days later, he did. Tom realizes she has blamed herself all this time for her father leaving, and she fears the same thing will happen again. He assures B'Elanna he will never leave her, and he hopes to have even more Klingon children and that every one of them is just like her. Later, Torres reverses the alterations to the Doctor, and while apologizing to him she feels the baby kick. Now she's happy about having a feisty Klingon in her womb. She asks the Doctor to be the child's godfather, and he elatedly accepts.