Returning from a diplomatic mission with Neelix, Tuvok picks up readings of a cloaked being within their shuttle, but while scanning it with a tricorder he is attacked. Once back on Voyager, Tuvok is rushed to sickbay suffering from neuroleptic shock. The Doctor treats the officer but cannot reverse the damage until he understands the nature of the weapon used against him. Captain Janeway questions Naroq of the Kesat species with which Neelix was negotiating, and the visitor feels certain the mythical Ba'Neth — or "shadow people" — were the ones who attacked Tuvok. Legend has it the Ba'Neth attempt to assess foreigners' technology, but stay cloaked because of an obsession with hiding their identity.

After gathering particles from the cloaking field, Naroq uses a photolitic converter to illuminate the isotopes and reveal what the alien looks like. Using the same idea with Voyager's deflector array, they are able to uncloak nearby Ba'Neth ships. In fact, there is an entire fleet surrounding Voyager and they begin to fire when hailed. Unfortunately, they are soon out of range and disappear again. Meanwhile, Tuvok's Vulcan brain has begun to rewire itself. When Neelix leads him on a tour of the ship to jog his memory, he speaks for the first time.

Although Tuvok is speaking and recognizing people again, his cognitive functions are still very simple. Experiencing volatile emotions, he tries to come to grips with the damage he sustained. When Naroq questions him about the cloaking frequency, Tuvok has a flashback but cannot remember any details. Soon, he becomes angry. After studying his personnel file and realizing how different he is from the Vulcan he used to be, Tuvok lashes out at Neelix.

Neelix realizes that instead of pushing Tuvok to be who he was, he should encourage him to discover who he can become. With this in mind, the two begin to have fun together. Tuvok discovers the joy of smiling and even tries his hand at baking desserts. When Janeway questions him again about the cloaking frequency, Tuvok cannot find the words to express what he saw. Instead, he draws it out in icing on his latest cake creation. Using that pattern, the Voyager crew begins scanning for the cloaking frequency.

Voyager discovers the hidden spacefaring civilization of the Ba'Neth, and Janeway demands information about their weapon. Once she threatens to transmit their coordinates to the Kesat, the Ba'Neth captain is willing to negotiate. However, he learns that Naroq is on board and prepares to fire. In a show of generosity, Naroq offers to give the Ba'Neth his photolitic converter in exchange for the information Voyager wants. After analyzing the weapon, the Doctor is able to devise a procedure that will restore Tuvok's Vulcan personality. Although he is quite fond of his crewmate's new demeanor, Neelix knows they need Tuvok at his post on the bridge more than they need a playmate. After the procedure, Tuvok resumes his logical and subdued manner, but he has learned to appreciate the word play of Neelix's riddles.