Two months later, Jordan pursues the man who promised her information, while her father is investigated for framing him. A serial killer is plaguing Boston. A new medical examiner joins the team. Lily returns to become the department grief counselor.
Jordan teams up with the new M.E., Elaine, and finds herself in the middle of an ATF power struggle, when she investigates the death of Wendy Marsh, wife of alleged Unabomber-style terrorist and former ATF agent Lester Marsh - whose grief and rage over the personal vendetta held against him by a former partner Agent Hawkes, pushes him to strap on some homemade explosives and hold the morgue hostage. Meanwhile, a personal quest for love in the crypt and some friendly advice drives a wedge between long-time mates, Bug and Nigel.
Jordan investigates the apparent heart attack of an kind, elderly man. When a mysterious individual tries to steal his body, Jordan suspects foul play and begins investigating. However, appearances are deceiving, and the man turns out to be a Nazi war criminal, who was murdered. At the same time, Dr. Macy is being investigated for a possible botched autopsy that occurred three years ago. As he struggles to remember the details, he fears his job is in jeopardy. While a new doctor investigates Dr. Macy, he investigates why he doesn't remember any details about the ...
Jordan and Bug team up with a new, obnoxious detective to investigate the murder of a man who only hours before was on a blind date with Jordan. Meanwhile, after a train car separates and ends up in the river, Garret and Lily work together to track down the families of the victims and Nigel must deal with survivor's guilt after narrowly missing becoming one of them.
Lily tries to be supportive to a mother who has lost her son through aids from an infected tattoo needle but Lily's tattoos cause the mother to shut down. Jordan meets with Dr. Stiles to discuss her past relationship with Tom Crane who's estranged wife has been found dead. Macy and D.A. Wolcott are called to examine the body of Roland Winton, a prisoner who was executed on death row. His parents believe his execution was cruel and want it investigated.
A young girl is seriously burned when a methamphetamine lab explodes. She later dies from her burns but it is then discovered that she had been shot and her actual cause of death is internal bleeding. Her mother blames her boyfriend Connor and vows revenge. Meanwhile, D.A. Wolcott informs the lab that Connor is an informant helping her to try and take down Freddie Paxton.
On a trip home to Kewaunee, Wisconsin a body falls from the undercarriage of a plane and lands beside Woody. It turns out to be the body of his former mentor - Sheriff Cody. He follows the evidence to Los Angeles but finds that he's not the only one that wants to solve the case.
Jordan investigates her new evidence seeking her mother's killer, leading to an abandoned vehicle trunk with a 23-year-old skeleton who turns out to be a missing cop who disappeared in 1979. Macy bans Jordan from having anything to do with the investigation so she enlists Peter to help her get information on a gun she found in the trunk and which she removed before the investigation started - which he later turns over to the D.A. as the gun is found to belong to Jordan's father Max.