When T'Pol is assigned a secret mission by the Vulcan High Command, she asks Archer to accompany her. The captain is surprised by her request, but agrees — especially when T'Pol reveals that there is a personal side to the mission. Many years ago, T'Pol was sent to retrieve several rogue Vulcan operatives. She was able to apprehend all but one of them, a man known as Menos. Now, the Vulcans believe they have located Menos, and they want T'Pol to bring him in.
Soon, T'Pol, Archer and Mayweather are on their way to the Pernaia system, where Menos was last spotted. As Mayweather pilots their craft, T'Pol briefs Archer on Menos: he was assigned to infiltrate a cell of smugglers, and apparently became one of them. Now, he reportedly makes a career of smuggling synthetic bio-toxins used to make transgenic weapons. T'Pol last spotted him on Risa, where she nearly caught him. Once the trio lands at the snowy alien outpost, T'Pol spots Menos in the crowded, bar-like shelter. Menos puts up a good fight, but Mayweather manages to apprehend him, and the trio prepares to take him aboard their ship. Unfortunately, the landing deck of the outpost is being thermalized, and they won't be able to leave for several hours.
Meanwhile, back on Enterprise, Trip is confronted with the difficulty of serving as acting captain. Both Phlox and Reed need him to make decisions that will affect the ship and crew, while Hoshi informs him that Enterprise has been hailed by the Vulcan Captain Tavek, who has an urgent message from Admiral Forrest. When Tavek insists on speaking to the captain, Trip pretends to be Archer. As it turns out, the message from Forrest consists of water polo scores, and a relieved Trip hastily thanks the captain and bids him farewell.
Back at the alien outpost, Archer, T'Pol and Mayweather are holding Menos captive until it's safe to take off. Menos tries to appeal to T'Pol, saying that he has a wife and two daughters and that he's really not a smuggler at all — he merely transports spent injector casings. As they continue to talk, Menos insinuates that he wasn't alone when T'Pol nearly apprehended him on Risa. This triggers some fragmented flashes of memory for T'Pol. In one vision, she sees herself chasing two men through the jungle; in another, she seems to be in emotional distress at a Vulcan monastery. Determined to prove that Menos is a criminal, T'Pol makes her way across the dangerous dock to his ship ... only to find cases full of spent injector casings. Frustrated, she returns to the shelter, and asks to speak to Menos alone. With his help, she manages to piece her visions into a coherent scenario. It seems that there was one other fugitive she was charged with retrieving: Jossen, whom she spotted on Risa with Menos. She chased both of them through the jungle, and ended up killing Jossen. Later, she underwent an obscure Vulcan ritual known as the Fullara, wherein her memories of the event and all the surrounding emotions were repressed. T'Pol reveals this to Archer, who is upset that Menos is manipulating her emotions.
With T'Pol's guard down, Menos manages to escape, and Archer, Mayweather and T'Pol chase him to his ship. Though Menos nearly traps them, T'Pol manages to apprehend him. As she trains a weapon on him, Menos appeals to her guilt — he insists that she will let him go, rather than killing another innocent man. Archer, however, reminds T'Pol that she was assigned to apprehend Menos — not judge him. The captain's words help T'Pol to come to final decision, and she brings Menos in. Meanwhile, Mayweather discovers that Menos actually was hauling more than injector casings — a large container of bio-toxins sits just beyond a hidden forcefield.
Back on Enterprise, Archer extends his sympathies to T'Pol, noting that her newly-resurfaced memories aren't going to be easy to deal with. T'Pol notes that she's ready to move on, and tells Archer that if he ever needs someone he can trust, she's there for him.