Chakotay is in sickbay, struggling to communicate with aliens through a vision quest. Through flashbacks, we learn of the events leading up to this scene. Chakotay is in a holodeck boxing simulation where he is knocked out. Shortly after, Voyager is pulled into chaotic space, an area where the laws of physics are in a constant state of flux. Seven of Nine warns that this type of space can easily destroy the ship due to changes in the gravitational coefficient. Chakotay begins to hallucinate, seeing his boxing gloves at various locations on the ship as well as hearing voices. He is taken to sickbay after attempting to fight Tuvok on the bridge.
The Doctor detects a genetic marker for a cognitive disorder in Chakotay, surmising that this is responsible for his hallucinations. Voyager finds another ship in the chaotic space, along with information that some of that crew was also hallucinating, suggesting that Chakotay's hallucinations may be induced by chaotic space.
Chakotay decides to go on a vision quest, hoping to learn more about his hallucinations. There he sees his grandfather, who had the cognitive disorder that has been reactivated in Chakotay. He becomes increasingly confused when the vision quest becomes a boxing match that he can't leave.
He is awakened by the Doctor, where he realizes that aliens were attempting to communicate with him through his vision quest. He struggles to communicate this clearly to the captain and the Doctor, as he continues to slip in and out of reality, returning to the boxing match again and again, as his mind had latched onto the boxing holo-program he had recently participated in. Chakotay fears he is endangering his sanity and safety, but decides going back into the vision quest is the only way to make first contact. He finally accepts a confrontation with his "boxing opponent." The alien sends information on how to escape, using the voices and words of the crew. Chakotay, back on his feet, manually adjusts the ship, being unable to actually explain it to Kim or the others.
After the ship is safe, Chakotay is given some time off, which he uses to further continue his boxing holo-program.