The crew of Voyager are foraging for food on a planet when Voyager, in orbit, detects a cloaked Kazon ship. Meanwhile, down on the surface is an away team who are looking at the different food sources the planet has to offer. Kazons are also discovered on the planet while the crew is evacuated to Voyager, except for Commander Chakotay who goes off to look for Seska, who is missing at the time. He finds her in a cave with a bag of mushrooms and a phaser pointed at him. She lowers the phaser as soon as she recognizes who it is and claims she thought he was a Kazon at first.
When back on Voyager, Seska makes Chakotay his favorite soup, mushroom. She begins to tell him that she and several other Maquis had taken the food to make the soup from Neelix's kitchen. At this Chakotay becomes enraged and disgusted. He asks her how she could take food from the rest of the ship like that. Neelix calls Chakotay and tells him that people have stolen food and he suspects Seska. Chakotay confirms his suspicion and says that everyone involved will be disciplined. He tells Seska that she will have her replicator privileges withdrawn for two days. She says they won't agree and he replies that they'll be thrown in the brig. He then walks over to the window in his room and stares out at space. Seska comes over to him and Chakotay tells her that they both agreed their relationship wouldn't work out. Seska becomes annoyed and leaves after this statement.
A few days later, Voyager detects a distress call from the Kazon ship they previously encountered, and discovers that a piece of equipment has caused a catastrophic failure on board, killing all but one crew, who is comatose. On investigation they find that the equipment bears resemblances to Starfleet technology, and realise that the technology must have been given to the Kazon by a member of the crew during the visit to the planet, and that this member of the crew must have been on their own on the planet's surface.
An engineering team goes over to the Kazon ship, but goes back to Voyager when they realize that they will have to discover what happened to the ship from Voyager (the Kazon ship has unstable elements in it). However, Seska decides to take matters into her own hands and to try to figure out what happened on the ship (she does this to prove her innocence), which causes her to go onto the damaged Kazon ship, even though it isn't safe. While on the ship Seska is injured and gets a scolding from her superiors when she returns.
Captain Janeway realises that the comatose Kazon may be the only chance of finding out how the technology came into their possession. Another Kazon ship arrives, and after attempting to convince Voyager to stop meddling in their affairs, the captain demands to see the Kazon crew member. During this visit, the captain covertly assassinates the comatose Kazon.
Meanwhile, Kes finds out that Seska has Cardassian DNA in her blood. Seska says the reason for this is because she had an illness as a child, and a Cardassian woman took pity on her and gave her the blood transfusion necessary for her to live. Kes doesn't believe this story and goes to the Doctor to see what he thinks.
Investigations reveal that a message was sent to the Kazon to organise a meeting on the planet. The nature of the time of the message implicates a member of the engineering team. The two most likely suspects are Ensign Seska and Lt. Carey. The senior crew members set a trap to identify the crew member, and Ensign Seska falls for the trap.
Seska explains that the Kazon are a powerful race in this quadrant and by giving them technology, Voyager will gain a powerful ally. Janeway retaliates by informing Seska that such careless sharing of technology could change the balance of power in the Delta Quadrant, and is forbidden by the prime directive. Chakotay accuses her of being a Cardassian spy on his ship. Seska then says that living with Starfleet had made him soft and that she had no clue how she could have ever loved him.
Seska, however, has pre-programmed a transport into the computer, and is beamed to a Kazon ship. Voyager is initially sent in pursuit, but more Kazon ships arrive and Voyager retreats.
In the last scene Chakotay sits down with Tuvok in the Mess hall. Chakotay asks Tuvok if he is extremely naive for letting a spy pull the wool over his eyes. Tuvok responds no. Chakotay then asks him if he had any idea that Seska was a spy. Tuvok responds that he had no idea and that Seska pulled the "wool over his eyes" as well. At this Chakotay smiles, and Tuvok asks him why both of them failing made him happier. Chakotay then responds: "Misery loves company, Tuvok".