Tom Paris talks his way out of a duty shift and goes to find B'Elanna Torres, who is working in a Jefferies tube. He presents her with some flowers and the two spend a little time kissing. B'Elanna is jumpy - she feels as though someone is watching them - but that seems to make it more exciting and she turns her attention back to Tom.
Meanwhile, Captain Janeway is receiving a therapeutic massage from The Doctor. She has been tense and agitated lately, and has been suffering excruciating headaches. Chakotay tries to give her a report on a powerful stellar phenomenon nearby, but she is too tired and grumpy to care so she tells him to just carry on as he sees fit.
Later, Tuvok seeks out B'Elanna to deliver a report to her. He finds her in Engineering making out with Tom Paris again. The two officers sheepishly attend a briefing with the captain, who angrily reprimands them for their inappropriate behavior. She didn't hear it from Tuvok, either. It seems the whole crew has noticed that the two lieutenants are having trouble keeping their hands off each other. Janeway demands they shape up.
Chakotay begins feeling strange as well. He begins shaking, loses all his hair, and starts going blind. Within a couple of hours his body ages many decades. Neelix sickens next. He breaks out in spots and begins to emit a strange odor. The Doctor determines that both men have had bits of their DNA stimulated by some external force. Janeway wonders if the energetic binary star phenomenon is affecting them somehow.
This theory is put to rest when the Doctor and B'Elanna scan the crew's DNA more closely. On visual inspection it appears that some of the nucleotides have been branded with alien writing, much like a barcode. While Neelix's affliction is described as something akin to "in-breeding", Chakotay's is said to suffer from Progeria, a form of premature aging. When B'Elanna tries to run further tests she is suddenly stricken with some sort of seizure and goes into respiratory arrest. Before the Doctor can reach her, his program is shut down.
As the remaining crew gathers to try to figure out what is going on, Seven of Nine receives a transmission from the Doctor, who has tapped into her auditory implants. He calls her to the holodeck, where he can make himself visible. He suspects that someone is implanting tags in the crew's DNA to cause mutations, and knocking them out when they begin to realize what is going on. He adjusts Seven's artificial eye so that she can scan for intruders on board. Indeed, there are several, roaming the ship invisibly, scanning and poking and prodding the crew without them even knowing it. Some of the crew have even been fitted with invisible appliances and implants to alter their physiologies.
Seven sees that Janeway has an array of huge needles jutting from her skull. The aliens place and remove them, and then note her response. Her headaches and psychological disturbances are getting worse. Seven attempts to sneak into the engineering computer to deliver a shipwide shock to disable the DNA tags, but she is caught. She has no choice but to fire on one of the aliens, making her visible. Tuvok takes her into custody and the crew continues to try to disable the tags.
A furious and unbalanced Janeway interrogates the alien in the brig, demanding to know why her crew is being tormented. The alien calmly explains that the Voyager crew are serving as valuable test subjects in medical and psychiatric research and are providing data that will help cure disease. She also notes that she has been very impressed with Janeway's self-control and high tolerance for psychiatric disturbance. She warns Janeway that if she doesn't allow her kind to be studied, the project and its subject would be terminated.
Janeway stifles the urge to inflict violence on the alien and returns to the bridge. However, when a member of the bridge crew is killed by the experimenters, Janeway will tolerate no more. She leaps to the helm and steers the ship directly toward the massive binary stars. As Voyager hurtles directly toward them, two alien ships attached to her hull become visible. Realizing the frantic Janeway is willing to let the ship be destroyed rather than allow her crew to serve as laboratory subjects any longer, the aliens depart the ship quickly. At least one of the alien vessels is destroyed by the intense radiation of the pulsars. Voyager shoots between the two stars and barely escapes through.
The crew begins to recover from their injuries and afflictions. Tom and B'Elanna get together for a date, and, free of any extra hormonal urges brought on by alien scientists, decide to do a little experimenting of their own.