The first thing that caught my notice was the dramatic phonecall in the lab between John and Sherlock, where John is afraid and Sherlock is leading John through what’s really all fake and set up by him.
Sherlock then releases John from the cage and the terrifying situation, which I believe represents what will be their reunion in Series 3, and maybe Sherlock helping John who’s suffering from Sherlock’s “death”. John yells “It’s not okay, I saw it…” at Sherlock, and Sherlock responded by telling John it was all fake.
^ Those parallels i’m all sure of, the rest is speculation about the content of Series 3:
Henry *KNIGHT (i called him henry fishguard oops) represents John after Sherlock’s death. He’s tramuatized over a memory of his father’s death, the details of which are falsely placed into his memory.
Dr. Mortimer, Henry’s therapist, represent’s Mary Morstan, who helps John through Sherlock’s death but ultimately fails when Henry tries to commit suicide.
Maybe John will try to commit suicide in Series 3, and Sherlock is going to run to his rescue?
Or maybe he’s just going to be incredibly mentally unstable, which Sherlock will lead him through with his return.
Either way, at the end of the episode everyone lives because the truth is revealed…