The serial killer known as "the surgeon" once tried to kill police officer Jane Rizzoli. When his signature killings recur Jane and the BPD team race against the clock to find his apprentice before he can kill again. Meanwhile, Jane and the Chief ME hide a huge secret.

When Jane and Maura find a baby girl left in a manger with a note from the mother that she would soon return, they temporarily take in the baby girl through the holidays while Jane searches for her mother. Meanwhile, Jane and Maura grow closer with the baby girl and each other with each passing day.