Knowing Sebastia is like climbing a ladder. But the thing is, it's a ladder that you don't move up on unless it allows you. And it doesn't so much allow you as it just drags you up a rung whether you like it or not.
Their first meeting, just after Sherlock's fall, was all cold, sarcastic flirting and heated death threats. John needed the truth, so he began looking for evidence that Moriarty was real. He needed evidence that it wasn't all a lie, not for himself, but for everyone else. Sebastia Moran was his evidence, and she was just as bitter about Moriarty's death as he was about Sherlock's. She shot him in the arm.
The next few meetings were caused by John chasing leads. Eventually she caught him and told him to leave her alone. There was more cold flirting, though not as cold as before. She drug him up a rung. She left him chained up in a warehouse.
They ran into each other on the street, and he called her out on her bag that was conveniently large enough to hold a deconstructed sniper rifle. She pulled a shoe box out with a new pair of heels with a smirk, but he saw a flash of metal. She yelled like they were a fighting couple and slapped him.
A few more meetings and a few more fights later she showed up bleeding at his flat. He let her in and played doctor with a gun pressed to his head. He insisted the gun wasn't necessary. She didn't believe him. She knocked him out.
The next time she showed up bleeding there was no gun. Up another rung. He patched her up without a word. No questions, no cold flirting. She kissed his head on the way out.
He started seeing her more and more, and it was okay. He was being drug up the ladder and he didn't mind, because she was chaos and he missed the thrill.