After Crewman Dalby shows clear insubordination towards Tuvok, he discusses the situation with Janeway. Janeway understands Tuvok's frustration but points out that the Maquis have never been trained in Starfleet procedures or philosophies. As such, 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. Tuvok, himself, will teach the class having been an academy instructor. At first this proves distinctly unsuccessful: the trainees, with Dalby as ringleader, walk out of their first lesson despite Tuvok ordering them to stay. Later in the mess hall, Crewman Dalby makes it clear to Chakotay that he wants to do things the Maquis way. Chakotay then punches Dalby, saying that violence is also the Maquis way. Chakotay says that if Dalby wants to do things in the Maquis way then so will he, by using violence to enforce discipline. Before leaving, Chakotay reinforces Janeway's orders. With his point made, the students return to Tuvok training sessions.
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. Tuvok attempts to get to know Dalby socially, though he makes little progress.
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 power 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 power 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. Tuvok orders the trainees to leave him behind and save themselves, stating that this is the most tactically sound move. The trainees are angered at his apparent disregard for their friend's life, and initially refuse, but Tuvok forces them out. He then contradicts his own order, going back into the poisonous gas to save the injured crewman, and in the process succumbs to the gas and passes out. 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.
The episode's principle plotline, dealing with Tuvok and his trainees, was originally devised as a subplot for another episode, until the writers decided that they liked it enough to make it the focus of an episode. The producers of the show were disappointed that Learning Curve became the default season finale due to scheduling issues with the season, describing it as "a run-of-the-mill episode...it wasn't a cliffhanger. It wasn't a season-ender. It had no bang. We just sort of disappeared." Schematics used to construct the sets for this episode were among the items sold off in the It's a Wrap! online auction of Star Trek items.