Unknown to John, Sherlock was pregnant at the same time as Mary. Sherlock refuses to tell John, not wanting John to hate him more or blame him for breaking up him and Mary. They are a family and Sherlock...is not. He can't take this away from John so he keeps quiet.

He keeps his distance from John and reasons he has two choices - abortion or adoption. Whichever he chooses (and *please* no judgement or bashing about whichever he chooses) he keeps a secret from John. Mycroft of course finds out and Lestrade, but they promise to keep his secret at Sherlock's uncharateristic pleading.

Fast forward two years, and Sherlock hasn't really seen much of John and has tried to move on until John comes barging back into his life. His marriage is over. He knows about Mary, about shooting Sherlock, and about Sherlock's baby. There is no baby Watson, no Mary, just John wanting to know why. How could he make such an important decision alone, why didn't he tell him?

And just like that, something breaks in Sherlock...and John is given the whole, raw, undiluted truth.

Bonus: Mycroft and Lestrade confront John after he barges back into Sherlock's life