Arriving in London almost 2 weeks after they'd left for the case, Sherlock left John at the airport and got a taxi straight to Molly's flat. Asking the cab driver to wait, he rang Molly's bell. When she opened the door, bleary eyed due to the late hour, Sherlock took a deep breath, cupped her cheek with his right hand, smiled at her and left.
The next time Sherlock finished his case, he went to meet Molly at Bart's. Again he just cupped her cheek, smiled and left without saying a word.
This became a ritual after every case. When Mary had her baby and Sherlock met Molly after seeing his new god child, Molly thought he blinked away tears from his eyes as he cupped her cheek and smiled and left.
When Molly was rescued from the hostage situation and the terrorist dealt with, Sherlock was literally shivering when he cupped her cheek. He took a shaky breath and left, barely smiling.
When he visited her next in the hospital, along with Mary, the baby and John, Molly saw him cup the baby's cheek in a similar fashion and kiss her when the Watsons were leaving.
When she couldn't help but ask him about this gesture, Sherlock hesitated and sat silent. Molly was surprised when he actually responded.
"The baby represents the innocence worth saving and fighting for. She is too young to be influenced yet and is all purity.
"You represent the good, the innocent, the honest and the loyal, in this world that I daily see and fight with. The fact that good and love can exist, in spite of all the negative forces that tell you its not worth it. You, Molly Hooper, represent everything in this world that is fighting what may seem like a losing battle, but still surviving.
"I look at you and I know that there is hope and what I do is needed, whether appreciated or not.
"I need to touch you to know that you really exist and that keeps me sane at some level and keeps that jaded outlook away.
"You have no idea how much that means to a man like me, Molly. "
As she sat stunned in the hospital room, Sherlock got up, kissed her on her forehead, cupped her cheek and left.