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=== Act Three ===
On the [[bridge]], [[Chakotay]] and Tuvok are arguing with Janeway about a [[Sumo]] match when The Doctor interrupts and accuses them of conspiring against him.

In the ready room, Janeway tells The Doctor that she had to deny him access to his memories of the events surrounding the attack because they caused a conflict in his programming that couldn't be resolved. The Doctor demands to know what happened, but Janeway tells him that that might cause the conflict to happen again. The Doctor feels violated because he has essentially been operated on without his consent, but Janeway believes that the ends justify the means and that rewriting his program again is the only option. She orders him to return to sickbay.

In sickbay, Chakotay asks for copies of The Doctor's memory files so that Torres and Seven can rewrite his program, and tells him to brief Paris about any experiments or tests he's performing, since Paris will replace him while he is off-line. The Doctor asks Paris why Janeway won't tell him what happened, and Paris says that she has her reasons and he agrees with her. 

Seven of Nine comes to Janeway's [[quarters]] late at night for a discussion on the nature of individuality. Janeway tells her that this isn't the time or the place, and to meet her in the mess hall tomorrow, but Seven says that tomorrow will be too late, since The Doctor's program will have been rewritten by then, and his rights as an individual violated. Janeway tells Seven that The Doctor is more like a [[replicator]] than like a person, and that she won't take the risk of his program self-destructing again. Seven counters that the doctor would disagree and muses that as a borg, she is also part machine, much like a replicator, and wonders if she might someday be treated in a similar fashion. Seven goes onto to describe how Janeway has been her "guide to Humanity", and then suggests she may have chosen the wrong person. Seven leaves Janeway's quarters, leaving Janeway with the realization what she has done to the doctor.

Janeway goes to sickbay and offers to show The Doctor what happened eighteen months ago. The Doctor agrees.