The fifth season begins with Lilly returning to work just weeks after being shot. She reopens a 1994 triple-murder case in which three boys were beaten to death. Two teens were convicted of the crimes but Lilly suspects they may have been innocent.

The 2006 murder of an Amish teen who left home to visit Philadelphia as part of rumspringa, an Amish rite of passage, is reinvestigated when the victim's sister arrives to look for her.