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John thinks that Mycroft is being extra™ and gets a phone call in a public phone box. John hops into the car and is kidnapped by Moriarty.
Sherlock isn't saved by John when the cabbie makes him take the pill
Moriarty brakes into the flat and kidnapped Rosie and John. Sherlock has 5 hours to find them
Moriarty, out of spite, blows John up.
Mary is one of Moriarty's assassins.
The CIA trained killers (in Irene Alders' house) shoot John. John survives but forgets a lot and Sherlock needs to help him remember.
"He really liked you, Sherlock. That's what killed him."