The premise of the episode is that of a group of cloaked aliens performing scientific experiments on the Voyager crew, and the effect the experiments have on the various crew members. The episode explores this from a third party perspective, and views the events in a manner similar to the medical experiments humans perform on lab rats or other animals.

The crew of Voyager note that Tom Paris and B'Elanna Torres have become intimately involved, while other crew report of small maladies to the Doctor, such as Captain Janeway, who has been suffering excruciating headaches. The crew initially attribute these problems to effects of a nearby stellar phenomenon, and continue on as they appear benign.

Over a matter of hours, Chakotay is aged several decades, losing his hair and going blind. Neelix suffers spots over his body and emits a strange odor. The Doctor and Torres finds that both have had their DNA stimulated by an external force, and discovers alien writing imprinted on their nucleotides like a barcode. However, before they can run further tests, Torres is overtaken by a seizure and goes into respiratory arrest, and the Doctor's program is shut down.

Seven of Nine receives a coded transmission from the Doctor, and she meets him in a holodeck. The Doctor explains that some entity is tagging the crew's DNA to force these mutations, and that the entity has the ability to silence those that come close to the truth. He adjusts Seven's optical scanners to detect outside the normal visual range. Seven starts going about her normal routines and sees a number of aliens, previously unseen, observing many of the crew which are outfitted with strange devices. Seven tries to alert Janeway without arousing suspicion but a female alien is observing Janeway's response to sleep deprivation using needles stuck in her skull. Seven covertly goes to Engineering to arrange for an energy discharge that the Doctor thinks will disable the DNA imprints. Tuvok detects Seven's tampering and orders her to cease and desist, attracting the attention of nearby alien observers. Left with no choice, Seven uses a phaser to disrupt the nearest alien's cloaking technology, making her visible, and captures her.

...
Wikipedia