John was actually the mastermind behind Moriarty's work all this time. He started the work ages before meeting Sherlock and rooming up with him was just a coincidence. Moriarty is either his most trusted second-in-command or his 'business' partner. Remember that swimming pool scene? It was a double-double cross with Moriarty happily playing his role while covering for John. After the Great Game event Sherlock still had no idea about John's identity.

Ending's totally up to the writer, make it comedic or angst or fluffy, as you will. Mild Johnriarty is great though my OTP is Johnlock.