As the Doctor takes holo-images of the crew, he finds evidence of neurosurgery he performed 18 months ago on Kim. However, he doesn't remember it. The Doctor asks Seven of Nine to help him run a self-diagnostic, but later he doesn't recall their conversation. Someone has ordered a deletion in his short-term memory buffer, and holo-images he took around the time of the surgery have been deleted. When Seven restores them, a female ensign they don't recognize is pictured with others in the crew, and one picture is of an alien on their shuttle.
Once Seven restores some of his memories, the Doctor recalls pieces of events from the pictures. When he remembers the alien boarded their shuttle and shot Kim and Ensign Jetal, he immediately tells Janeway. She agrees to investigate but tells the Doctor to deactivate his program for the time being. Before he does, he orders the computer to take holo-images of anyone who accesses his files while he is off-line and then reactivate him. Shortly, someone comes into sickbay to delete more files. When the Doctor develops the holo-images taken, it is Janeway.
The Doctor confronts Janeway, who tells him that he was damaged during the incident with the alien. It caused a conflict in his program, so she was forced to restrict his access to memories of that period. The Captain refuses to tell him what happened, and now that he is starting to remember, she plans to rewrite his program. After Seven challenges her decision and she has had some time to think about it, Janeway agrees to restore his memories.
Scenes from the pictures come to life. The Doctor, Kim and Jetal were on a shuttle mission when an alien ship attacked. Their shuttle was boarded, and the alien shot Kim and Jetal. Once Voyager beamed them to sickbay, the Doctor discovered the alien's energy pulse had remained in their neural membranes, and the only way to save them was to isolate the spinal cord from the brain. There was only time to perform one procedure, and the Doctor chose Kim.
After Jetal's funeral, the Doctor began having a breakdown. Now that he has remembered everything, he begins agonizing over the same question of how he could choose one life over another. There is a battle going on between his original programming and what he has become. The crew keeps vigil with him, hoping that eventually he will forgive himself and learn to accept his decision.