After Crewman Dalby shows clear insubordination towards Tuvok, a class is organized to teach several previously Maquis crew members proper Starfleet protocol so that they can integrate more fully with the rest of the crew. At first this proves distinctly unsuccessful, with them walking out of their first lesson against Tuvok's direct orders. Later in the mess hall, Crewman Dalby makes it clear to Chakotay that he wants to do things the Maquis way. Chakotay then promptly punches Dalby, saying that violence is also the Maquis way. With his point made, the students go to every future session with Tuvok.
When Tuvok shares with Neelix that he is frustrated with the Maquis' unwillingness to adapt to Starfleet protocol, Neelix indicates that perhaps it is Tuvok who is being inflexible in his strict adherence to procedure, and that perhaps if he were to "bend the rules" a little bit, the trainees would respect him more.
Meanwhile, it is discovered that the bioneural circuitry that runs many of the crucial systems on the ship has become infected with disease. Tuvok and The Doctor trace the infectious agent back to a batch of homemade cheese that Neelix had prepared. The Doctor discovers that the only way to kill the microbe is to heat up the bioneural gel packs, essentially giving them a fever to fight the infection. The crew runs the warp core at 80% without going to warp, which produces enough heat to kill the virus; however, it also initiates a pulse surge, causing many conduits to be blown out.
At that moment, another class is in progress in a cargo bay, but still with little progress in reforming the students. However, when a conduit blows in the cargo bay, they must work together to get out before the room fills with noxious gas. They succeed, however one of the trainees is injured in the explosion. Regardless, Tuvok orders them all to leave him behind in the cargo bay in order to ensure their own safety.
After getting the other trainees out, Tuvok contradicts his own order by going back into the poisonous gas to save the injured crewman; however, in the process he succumbs to the gas and passes out. However, Dalby and the other trainees work together to rescue Tuvok. After the incident is over, Dalby indicates to Tuvok that if he is willing to bend Starfleet protocol to save one of them, perhaps they can bend to accept the Starfleet rules after all.