When a Maquis engineer named Dalby disrupts power to the ship's energy grid by making an unauthorized repair, Janeway realizes that she can't expect Starfleet behavior from people who never went to the Academy. To bring the Maquis officers up to speed on Starfleet protocol, Janeway asks Tuvok to train a group of four recruits, including Dalby. Predictably, the Maquis recruits balk at Tuvok's by-the-book discipline until Chakotay forcefully gets the point across that this is not a voluntary exercise.
Like any good drill sergeant, Tuvok comes down hard on his Maquis charges, demanding regulation attire and behavior. Dalby complains to Torres about Tuvok's tough tactics, but Torres suggests that Dalby is afraid he can't cut it. The conversation is abruptly halted, however, when one of the ship's bio-neural gel packs malfunctions, the second time in days. Torres takes the pack to Sickbay, and the Doctor notes that the partially biological component has an infection and must be "cured" before it spreads to the rest of the ship's systems.
Tuvok's rigorous training sessions seem to work at a superficial level, but the Maquis are easily discouraged. Tuvok confesses to Neelix that he doesn't understand why his techniques, honed through years of instructing cadets at the Academy, aren't working. Neelix advises Tuvok to be more flexible in his approach.
While pondering the Talaxian's advice in the mess hall, Tuvok wonders if bacterial spores from Neelix's newly made homemade cheese is being absorbed by the ship's ventilation ducts, serving as the source of the gel pack's infection. The Doctor inspects the cheese, and Tuvok's hunch turns out to be correct.
Not long after, Tuvok and his students find themselves trapped in a Cargo Bay when another system falls victim to the virus. When the Voyager crew infuses the gel-packs with a plasma burst of heat to kill the infection, noxious vapors leak into the cargo bay where Tuvok and his recruits are stranded. Nearly overcome by the fumes, Tuvok helps three of the four cadets escape, then goes back for the incapacitated fourth. As the toxic gas ultimately overcomes him, his three black sheep finally band together to become an effective team, forcing open the door and rescuing both men. Later, Dalby notes that if Tuvok can break the rules sometimes, then maybe they could learn to follow protocol under his tutelage after all.