Molly had always known that he is going to come after her. She never really believed that Moriarty would just die, after all, he is similar to Sherlock in many ways. She always knew that he would come for her once he realizes Sherlock didn't really die. He had thought she didn't matter to Sherlock, that she is not important to him at all.
In many ways, she wasn't.
Sherlock did not want her friendship nor her love. He wanted her skills as the pathologist, and during the three years of being dead, she became his nurse. He would come to her when he was truly desperate, and would compliment her in an effort to get what he wants. He would never need her.
(He didn't really need to. She would have given him anything he wants.)
Many people she knows cannot believe she loves Sherlock. They believed that she fell in love because of how he looks, and maybe a part of her believes in that too. But there is a bigger part that believes she fell in love with his intelligence. She always amazed the way he would make the deductions to solve the cases, and how he is brilliant in it. She knows exactly how cruel and unemotional he can be, after all, she has been at the end of his deductions many times.
Still, no matter how many times he crushed her heart, she would love him. And will do anything to keep him safe and happy.
And that's how she found herself standing on the edge of the of St. Barts. One step back and she will fall into her death, just like Sherlock did three years. Besides her is John, who looks pale but determined. James Moriarty is standing in front of them, with his back to him while he gloats at Sherlock. She can see a red dot right on top of John's heart and knows she is in a similar situation. Sherlock's face is blank, but his eyes expresses a panic she had seen only at the day of her fake death. She then knew that Sherlock may not be able to solve this case.
"C'mon Sherlock, did you really think I would not have a plan? I knew you have some trick, but I never thought that would involve mousy Molly Hooper," Moriarty said. He turns to look at her, and she tries not to shiver at his evil grin.
"I underestimated you Molly Hooper."
(She has always been underestimated. She has always been known for being weak and romantic.)
"Now is your choice, the final game Sherlock," Moriarty says and he turns away, and Molly couldn't help but give out a relieved sigh. "You can only save one Sherlock. Ooh, who would it be? John Watson, your friend, or Molly Hooper, the one who saved you? Oh this is so much better!" He said manically. Sherlock seems to find no plan and she can see the panic clearly now.
"Tick tock Sherlock! You only have two minutes, or my gunmen would shoot both of them. C'mon Sherlock, only one can be saved. And do anything heroic, both of them will die if you attempt to hurt me. What's your choice Sherlock?" Moriarty continued to gloat.
Honestly, Molly cannot remember how she even got here. One moment she was in the lab the next she is now standing at the highest floor, and step away from death. But it does not matter; the only thing that matters now is how to get out of this situation. She is not ashamed by the fact that she wants to live, after all, it is a basic human instinct. However, her mind suddenly brought up the picture of John, Sherlock and Mary at the wedding. Oh God, Mary and her unborn child needed John. She had completely forgotten about her. She knows how much John and Mary love each other, and Sherlock's acceptance and friendship with Mary had made her part of the group.
If, by a miracle, Sherlock did choose her, how could she live with the fact that John died because of her? Could she live with the fact that the child would never know about his/her father? Could she live with the fact that Mary lost the love of her life because of her? Could she live knowing that Sherlock needs John and his friendship?
No, John was important to many people. She was underestimated and unimportant. She did not count. At all.
She knew what she had to do. She realized the tears now coming out of her eyes, but didn't stop them. She looks at Sherlock and sees how desperate and vulnerable he looks. No, she could not let that happen. She cannot let him choose. She cannot let him get this hurt.
"Sherlock," she whispers. He looks at her, his beautiful eyes trained at him. She gives him sad smile. "I love you," she whispers.
Moriarty looks at her, thinking she is begging for him to save her. Oh how much he has underestimated her.
Before anyone can even blinks, she takes that one step. She falls to her own death.