There is a neurological condition known as Capgras Syndrome. It occurs in people with pre-existing PTSD or some forms of mental illness after that person has a head injury and causes a person to believe their friends and loved ones are imposters. I'm thinking, John somehow gets a head injury, don't really care how, could be from a criminal they're chasing, a car accident, Sherlock accidentally hits him, etc. Anyway, after a blow to the head, John develops Capgras Syndrome, thinks Sherlock, Mrs. Hudson, Lestrade, Mary, and possibly Mycroft, are all imposters and he tries to kill all of them to bring back his real loved ones, except there's no imposters and he tries to kill his actual loved ones. Sherlock and Lestrade try to figure what is wrong with John and why he is trying to kill them. Please don't actually kill any of them, but some major whump, especially Lestrade( I'm a fiend for Lestrade whumpage, as long as someone's there to comfort him after)would be greatly appreciated.

Also, Capgras only has an effect on people who are close to the person that has it, so John would not see Donavan, Anderson, or possibly Molly as imposters.

I don't really care how the imposters are manifested, they can be drones, aliens, clones, whatever. I just really want this.