At his cottage, Number Six is participating in an ESP test with Alison with a high number of successes, demonstrating they are in mental simpatico. She takes a picture of him for the upcoming Village festival and knocks a bottle onto his finger, bruising his nail. She takes two photos while Number Six congratulates her on her success. He ushers her out for the night and goes to bed.
In the observation chamber, the new Number Two monitors orders the use of a device to place Number Six in a deeper sleep. A team of technicians administers a sedative and transport him to a laboratory where they burn a mole off of his left wrist, then use an electrical prod to condition him into becoming left-handed.
Number Six wakes up in a different bed in a different cottage to discover it's only a day later and he now has a mustache. His Village badge has the number 12 on it. Number Two calls and invites him to breakfast, referring to him as "Number Twelve." Everyone on the street refers to him as Number Twelve and claim he's always been called that. Arriving at the Green Dome, Number Six meets with Number Two and offers him breakfast. Number Six discovers he now likes flapjacks and asks what is going on. Number Two explains that he had "Number Twelve" brought in special to break Number Six. Number Six plays along as Number Two explains the plan, and mentions "Susan" never liked him with a mustache. Number Six discovers that he's left-handed, and Number Two has Number Six's mustache trimmed and his hair styled to resemble… Number Six.
Number Two takes Number Six to Number Six's cottage, and Number Six says some small things have been changed. Number Two gives Number Six a password, "Gemini," to identify himself, and leaves. "Number Six" arrives shortly thereafter, wearing a white jacket. The two men spar and the real Number Six has trouble due to his left-handedness and the fact he no longer can smoke cigars. "Number Six" suggests they have a shooting match to test their abilities but the real Number Six fails when he's obliged to use his "wrong" hand to continue the impersonation. Next they fence and the real Number Six loses. As they leave, "Number Six" throws a punch at Number six who again can't keep up when he can't decide which hand to favor.
They're interrupted when the white sphere arrives to escort them both to the Green Dome. Thugs take "Number Six" away while Number Two welcomes Number Six with welcome arms as the impersonator. Number Two has "Number Six" tortured while the real Number Six looks on. "Number Six" finally collapses from the strain. Number Two then uses a fake fingerprint projector: it displays the real fingerprint on a side screen which Number Six sees, but a mismatch on the overhead projection. "Number Six" insists it's a fake and Number Six backs him up, calling in Alison to demonstrate their psychic link. Alison arrives and conducts the ESP test… and Number Six fails. "Number Six" goes through the same test and succeeds flawlessly. Alison also points out the real Number Six has a mole, but the real Number Six doesn't and "Number Six" does. "Number Six" escorts Alison home while Number Two berates Number Six for relying on Alison to prove himself. Number Two also calls up the technician who was supposed to apply a mole to Number Six and failed to do his duty.
That night, Number Six is in his cottage having a nightmare. Numbers Two and Twelve look on as Number Six starts to crack. He wakes up later that night and notices the bruise on his fingernail has grown out. He checks the photo that Alison took, supposedly a day ago, which shows the bruise much closer to the base of the nail. Realizing he's been unconscious for several weeks, Number Six concentrates and recalls the programming that he underwent to make him left-handed, give him an appetite for flapjacks, and a distaste for cigars. He checks the cigars and discovers a wire used to taint the flavor.
His memories restored and his identity confirmed, Number Six now has to regain his right-handedness if he's to become whole again. Holding a faulty lamp in one hand, he grasps a metal fireplace fitting and shocks himself, breaking the conditioning. He goes outside and makes his way through the Village. Meanwhile, Number Two tunes in to Number Six's cottage and discovers him missing.
Number Six runs into two thugs who demand the password from him. When he gives the password "Gemini," they attack him but he readily defeats him. When the guardian sphere closes in, he gets in a cart and then sends it off without him. While Number Two calls for Orange Alert, Number Six confronts his doppelganger (the real Number Twelve), who is armed with a nerve gas gun. Number Six feigns mental confusion and asks Number Twelve who he is. Number Twelve asks him why he resigned but Number Six gets close enough to disarm him. The two men fight and Number Six proves triumphant. He forces Number Twelve to give him the real password, "Schizoid Man," and reveals that he has a fake mole. Number Twelve runs outside to find the guardian sphere waiting for them. Both men know the proper password, but Number Twelve panics and runs away. The guardian sphere assumes he's the imposter and kills him.
Number Six calls Number Two and gives the proper password, then tells him that "Number Six" is dead. The next morning, Number Six dons the white jacket and goes to the Green dome. He tries to bluff his way through the situation as he is to be put on a plane to report to their superiors. Number Two wants Number Six to talk with Alison to see if she has any insights into Number Six's mind. She doesn't, but Number Six briefly gives himself away.
Number Six prepares to leave, finding a photo from Susan in Number Twelve's jacket. As they go to the helipad, Number Two notices something amiss and comments on Susan saying something a month ago. Number Six agrees with him. They arrive at the helicopter where Alison is waiting. She admits she's ashamed of what she did to Number Six and wouldn't do it again, and keeps his secret. As Number Six gets in the helicopter, Number Two asks him to give Susan his regards and Number Six promises to do so.
Number Six dons a blindfold and the helicopter lifts off, flies briefly, and then lands. Number Six removes the blindfold to find himself back in the Village. Number Two is waiting… and informs him that Susan died a year ago.