Tuvok and Neelix have returned from a diplomatic mission concerning two races in conflict. Tuvok scans the shuttle used on the trip, discovering a cloaking frequency, and suffers neurological damage after an attack by an invisible alien. He experiences cognitive impairment, memory loss, personality changes, and loss of emotional control. With help from the race they had just met with, Voyager receives a deputy investigator with theories on the terminally cloaked alien race, allowing Voyager to expose them.
Neelix resolves to help Tuvok recover. In the process, they develop a deep friendship, one that Neelix has desired but Tuvok has till late denied. As Tuvok's recovery ensues, he slowly is able to recall details of the encounter, as well as discover new abilities in himself such as preparing desserts and enjoying jazz.
The information locked in Tuvok's damaged mind is essential to resolving the conflict between the two alien races. Neelix must also work with the conflict of what Tuvok needs, what Neelix himself desires in his new friendship, and what the crew of Voyager itself needs out of their formerly expert tactical officer Tuvok.
Following Captain Janeway's encouragement, Tuvok eventually draws the cloaking frequency in icing on a cake he prepared, and the crew is able to produce this frequency through the deflector. They expose a cloaked space station, and eventually negotiate for details on the weapon used on Tuvok. Tuvok eventually makes a full recovery, but appears to still retain a bit of the illogical self he briefly knew.