Dr. Crusher holds little hope for the recovery of the patient she has dubbed "John Doe," but he soon begins to exhibit amazing recuperative powers. While his damaged tissue is repairing itself at a remarkable rate, "John's" undamaged cells are mutating in a manner incomprehensible to the doctor.

Evidence surrounding the pod's wreckage indicates that it was involved in a battle, but when "John" awakens, he is unable to remember anything from his past. When Picard tells him that they have nearly determined the coordinates of his origin and that he will soon be returned to his planet, "John" experiences a sense of fear and tells Picard that he thinks he was trying to escape his planet, but cannot remember why.

Meanwhile, "John's" presence seems to bring a sense of serenity to the crew members he is in contact with, particularly Geordi. "John" then exhibits remarkable powers when he heals O'Brien's dislocated shoulder with a touch of his hand, which emits the same wave of visible energy that entered Geordi.

"John," however, is soon plagued by intermittent bouts of severe pain which frighten him into trying to steal a shuttlecraft. When Worf tries to stop him, "John" suddenly convulses in pain and then pulses into a large flare, knocking Worf off a catwalk to the deck below. Dr. Crusher's examination of Worf shows a broken neck and no vital signs, but when "John" touches him, a glow of light again emanates from his hand and Worf is completely healed.

When Dr. Crusher reports that "John's" rate of cell mutation is increasing, he fears that he will be dangerous to the crew and asks Picard to let him leave. However, their conversation is interrupted by the approach of an unidentified vessel which begins scanning the U.S.S. Enterprise. The commander of the ship, Sunad of Zalkon, demands the return of "John," declaring that he is an escaped prisoner sentenced to death for acts of agitation.

Having no memory of the past, "John" can neither confirm nor deny the accusation, but offers to surrender in order to prevent endangering the U.S.S. Enterprise. When Picard refuses to turn "John" over, the entire crew of the U.S.S. Enterprise is suddenly struck with paralysis. Realization of his past slowly dawns on "John" and he calmly departs for the Bridge where, by touching a console, his energy spreads to cover the entire starship and heals the crew.

With a wave of his hand, "John" brings Sunad onto the Bridge and explains to Picard that his species is on the verge of an evolutionary change and that the rulers, fearing a loss of power, began to destroy the first members to go through the metamorphosis. Sunad is then returned to his ship and "John," having evolved into a form of energy, prepares to return to his people to spread the word of the coming rebirth.