Voyager approaches a nebula which extends far beyond the ship's sensors. Captain Janeway decides to try to go through it rather than around, but within minutes of entering the nebula the crew begin to suffer mysterious burns. Janeway orders helmsman Tom Paris to turn the ship around, but he collapses in pain before he can execute the command. Tuvok makes it to the helm and plots a course back out of the nebula. Seven of Nine, who had been unaffected, arrives on the bridge to help tend to the crew but discovers one ensign has already died from severe burns.
Janeway heads to sickbay where the Doctor has been studying a sample of the nebula's gases. He tells her that the damage came from subnucleonic radiation and that even the briefest exposure destroys organic tissue. After exploring all options, he says the only protection the crew has against the radiation would be to go into stasis. Janeway is initially a little unnerved by this, but the Doctor assures her that he is perfectly capable of handling all the ship's systems. The Captain points out that he needs backup in case his holomatrix goes offline, to which the Doctor replies that Seven is apparently resistant to the effects of the radiation, and she can assist him.
The Captain then calls a meeting of the senior staff and informs them of the situation. She explains that Seven and the Doctor will check on them four times a day, and that when they awaken a month later it will simply feel as though they had taken a nap. Chakotay is initially uncertain about Janeway's allowing Seven responsibility for the lives of the crew, but the captain reassures him. The crew enters stasis.
The first few days through the nebula are uneventful and Seven develops an efficient routine of maintaining the ship's systems and monitoring the crew. Then, one day, she comes across Paris lying in the doorway, unconscious, and unburned by radiation. The Doctor arrives to help put Tom back into stasis and tells Seven it's not unheard of for people to come out of stasis early and to begin wandering. Seven becomes annoyed with the Doctor and he suggests she spend some time on the holodeck to relax and practice interacting with people.
The program the Doctor picks out is a crew party which takes place in the mess hall. Instead of mingling, Seven stands off to the side trying to figure out how to recalibrate the warp field in order to resist the nebula's radiation. When the Neelix hologram comes over to try to get Seven to join the fun, Seven decides the program may not be a complete waste of time after all, and asks Neelix, who has some knowledge of warp field theory, to assist her. She then invites Janeway to help with the calculations as well. The Doctor freezes the program, explaining that doing math is not an appropriate activity for a party.
Suddenly Voyager is rocked with explosions. The computer warns them that the anti-matter storage tanks are failing. They leave the holodeck and find that they will have to eject the tanks. The Doctor heads to the bridge and Seven to Engineering. The Doctor detects that Engineering is filled with plasma and is about to experience a hull breach, and warns Seven not to go inside. She ignores him and heads in to try to eject the anti-matter tanks. She finds that everything is normal, and the meltdown was a false alarm.
As they go to repair the alarm system the Doctor's program begins to degrade. His mobile emitter has been damaged by the nebula's radiation and he will now be confined to sickbay. Seven is on her own.
By the twenty-ninth day in the nebula, Seven begins feeling the effects of prolonged isolation. She has disturbing dreams, and visual and auditory hallucinations. She sees the crew dying and crying out for her. She tries to keep going.
The ship encounters another vessel with an alien on board. He introduces himself as Trajis Lo-Tarik and requests a trade for supplies. Seven allows him to come aboard Voyager and they negotiate a trade. The alien talks to her, suggesting she must feel lonely and isolated without her crew, and especially because she's ex-Borg and she's used to hearing the thoughts of millions of others. Seven becomes anxious and suspicious and pulls a phaser on Trajis. He disappears.
She feels he may have been a hallucination but reports to the Doctor that he may have also been a real intruder and she needs help. He can't assist from sickbay so she'll need to handle the situation herself. Seven arms herself with a plasma rifle. She continues to hear the crew and Trajis calling for her. Trajis begins taunting her, threatening to breach the ship's warp core. Now he's on the bridge and has complete control. Seven suddenly hears Paris' cry for help from the upper level and rushes to help him, but as soon as she reaches the top of the ladder she sees both Paris and Harry Kim burst into flames.
Seven cuts off oxygen to the bridge and listens to Trajis die. Soon thereafter, he appears in Engineering and continues taunting her. The Doctor succeeds in hot-wiring his mobile emitter and comes to help Seven. He assures her there is no one else aboard the ship. Before his program shorts out again, he encourages Seven to hang on.
Seven, alone, suffers more nightmarish hallucinations in which the crew taunts her. Propulsion systems fail, and Seven is forced to choose between re-routing power from life support or stasis support. She chooses to route power from life support, and finally passes out. She awakens to find the crew safe and healthy and out of stasis to welcome her back.
Later, Seven watches as Paris and Kim chat with Torres in the mess hall. She surprises them by asking if she may join them. She tells them that she feels the need for companionship, to which Paris says he can understand after being stuck with only the Doctor for company for a month. Their conversation turns to the fact that Paris left his stasis unit on four separate occasions and had to be put back in, which elicits some teasing from Kim. Paris says he doesn't know why, but he doesn't like closed spaces. Seven suggests it is because he dislikes being alone.