John has been working for Moriarty the whole time (absolutely willingly, please, without any abuse towards John, or anything of that sort!). Maybe he was Sebastian's captain in Afghanistan, and Sebastian still obeys him.

Jim needs to get a bit closer to Mycroft and a bit of spying, so he gives John a mission to get close to Sherlock. The first encounter with Sherlock is set up (maybe Mike is in it, too). Bonus if Sherlock falls in love with John. John can be sincerely protective of Sherlock; after all, Sherlock is his mission.

Later, after Sherlock's fake suicide, Jim sends John one of his assassins (Mary), as a present (well, sort of. Mary doesn't object), so John won't get bored, while his plaything (Sherlock) is away. I.e. John knows Sherlock is alive. Mary can actually become John's girlfriend and fiancée. Or maybe they are just friends pretending to be a couple.

Meanwhile, Sherlock isn't busy destroying Moriarty's web, no. Unknowingly, he destroys Moriarty's rival gangs instead, and Moriarty throws him some fake information the whole time.

When later the truth about John is out, Sherlock's heart shatters.

Please, no insanely evil John. He's dark, but not psychotic. I also prefer no bad endings for John or Mary.