What if things were different?
Molly met Jim at a moment when they both didn’t need it. Or so she thought.
Time passed, and they got close. More close than she thought they’d could. Too close. He changed her, taught her to not play it safe all the time.
He cared about her. More than he was supposed to. When he realized he couldn’t go through with his initial plan, he said he will do anything to keep her close till everything ends.
He told her the truth. That it started as a fake relationship, a part of his plan. When it was time to screw things up so that she’d dump him, he couldn’t. He wants her and nothing will come between them, not even his hate for her precious Sherlock.
He will not back down, tho. He will end his plan.
Molly was scared. She thought about it. While she listened to Jim, explaining his plan in detail, she realized he understands him.
So she helped. Molly helped Jim kill Sherlock Holmes.