During his ordeal in the Embryo Room during the episode Once Upon A Time, Number 6 admitted that he killed - killed for peace. So had, Number 6, like James Bond, been "licensed to kill?" He might have had a brilliant career, but had "killing" given him a conscience, like Callan? And is that why in the opening sequence to Living In Harmony we see the Prisoner handing in both his badge and gun, the reason he gave the Judge were "his reasons."
During his ordeal in the Embryo Room, Number 6 has a fencing foil, the protective tip of the blade comes away and he has a chance to "kill," in fact Number 2 orders Number 6 to "Kill! Kill boy. Go on kill !" But Number 6 couldn't do it, he couldn't kill, through cowardice, or conscience?
The order to kill by Number 2 could signify that Number 6 in his highly confidential, top secret job had been order to kill. But I don't think that Number 2's suggestion that, "You won't step over the threshold because you're scared! Your resignation was cowardice, wasn't it?" holds any water. Part of Number 6's resignation might have been for peace, "for peace of mind," but Number 6 was no coward. He's proved his bravery in the village on several occasions.
As to why Number 6 could not kill Number 2 on command, but only injure him, might lie in the fact that he was beginning to like Number 2. After all Number 2 admitted as much to the
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