Molly's first two dates with Jim were too good to be true. By their third date, she knew something was amiss. Sherlock thought Jim was gay, although Molly doesn't believe that. Still, she can't shake the feeling that Jim is hiding something from her – something big. She remembers her mother's advice about men. "If your instincts tell you something's off, it probably is." (She was usually right about people. She told us to stay away from Travis Nabors, and he wound up in prison.)
Molly squares her shoulders and picks up her mobile. She isn't normally the sort of person who breaks things off over the phone, but in this case, it seems like a good idea. She dials Jim's number and stammers out something along the lines of "this isn't going to work out." Jim is surprisingly calm, but then, they did only have three dates. Molly doesn't give him another thought until a few nights later, when her phone rings at 2:30 AM.
The pathologist is stunned to hear John Watson on the other end. There's a very uncharacteristic edge to his voice when he asks Molly if she's OK.
Molly's greatest fear is that whatever happened to Sherlock and John is her fault.