The Delta Flyer, occupied by Seven of Nine, The Doctor, and Ensign Harry Kim, flies by a comet that contains primitive DNA. The Doctor beams a small sample of it on board. The ship shakes a few times, and The Doctor complains.
Unbeknownst to them, they are in violation of local law by having The Doctor on board. The aliens, who are called the Lokirrim, believe him to be a "photonic insurgent" and when he is detected they begin to decompile his program. Four aliens beam onto the Flyer demanding to know where the "photonic" is. When they reach the rear cabin, Seven states that he was murdered by their disruption beam. The four Lokirrim take Seven and Kim under arrest.
In the detention cell, Harry furiously bangs on the wall. Seven is acting perkier than she has ever been. Kim decides that things can't go worse because of the multiple things that have gone wrong. Seven tells him that she is actually The Doctor. She downloaded him into her cybernetic matrix using her Borg assimilation tubules so he wouldn't be destroyed by the Lokirrim. The Doctor experiences human senses such as smell and touch for the first time.
Back on Voyager, Lieutenant Tom Paris scans over Tuvok with a tricorder. Tuvok suggests a medicine that will help him, but Paris must deny his request because he is not the chief medical officer. Tuvok explains that his libido is increasing rapidlyâin other words, he's going through pon farr. Paris reassures him that he'll tell the captain that he has the flu and will be out of commission for a few days.
Seven/Doctor is enjoying the exquisite and delectable taste of prison rations (although Harry suggests his uniform would taste better). The aliens call Seven to the Delta Flyer. The captain of the alien vessel, Captain Ranek, asks about the food replicator and if it can create bioweapons. She replicates a slice of New York cheesecake. The Doctor then fully enjoys the sensations of taste and eating by gorging on various foods and drinks, including no fewer than nine glasses of wine.
Seven/Doctor later stumbles into the detention cell drunk, but with the mobile emitter in hand. The Doctor uploads his program back into the mobile emitter, only to bring back Seven of Nine who is outraged that the Doctor "abused" her body. The Doctor is not able to say much as he is at a loss for words. Seven is thoroughly distraught at the fact that she has to have The Doctor take over her body again.
Paris checks in on Tuvok. The medicine that was used last time was not working. Tom suggests the holodeck to relieve him of the urges. Tuvok is appalled by the offer, feeling that doing so would be like cheating on his wife T'Pel; Tom suggests that Tuvok create a holographic version of T'Pel, an idea which Tuvok reluctantly accepts. While Tuvok is in the holodeck, another Lokirrim ship disrupts the holodeck because of the photonic activity. They begin the search for the Delta Flyer and its occupants secretly as they are escorted out of Lokirrim space.
The Doctor is treating several patients in the medical bay when he is called to the bridge by Ranek. He wanted Seven to see a spectacular view of a pulsar cluster. Ranek kisses the totally unprepared Seven/Doctor. Seven storms off to the medical bay again. There she seeks treatment for a muscle spasm, and gets a massage from the physician, Lieutenant Jaryn. The Doctor then experiences another sensation, sexual arousal.
When she gets back to the detention cell, he uploads his program into the emitter again, and once again, Seven is furious. They start arguing over their humanity, but Kim breaks them up. Fortunately, Seven was able to study the ship's systems and was able to devise a way back.
Seven allows the Doctor to take control of her body again. He has just invited Captain Ranek to the Delta Flyer for a dance and dinner. She sedates him during a waltz. She then hails Voyager. Captain Janeway, along with the rest of the bridge crew, is utterly confused as to Seven's condition at first, although they quickly learn that 'she' is currently the Doctor.
Voyager sets a course for the ship that has them. Tuvok disables their escort and jumps to warp.
Seven is back in the medical bay with an unconscious Ranek. Jaryn revives him. Ranek immediately orders Seven to be taken to detention, but the bridge hails that an alien ship is approaching. He negates his previous order and has Seven brought to the bridge. Janeway hails them, but is forced to use the command codes to disable the shields. Ranek ties the shields into the warp matrix. Seven then rematerializes the Doctor.
Ranek tries to reinforce the failing shield grid, but ends up being injured in the process. The Doctor stays behind to treat Ranek. They briefly talk and The Doctor explains that he was actually the one that the crew was interacting with.
Tuvok is grateful for Paris' help, but has one small problem: the hologram of his wife was inaccurate. Her ears were four millimeters too small.
Meanwhile in sickbay, Seven decides to have a meal with The Doctor so that he can once again enjoy eating, albeit vicariously as Seven describes the sensations.