After being on sabbatical for three months, Megan comes back to work after Peter's death. As she begins the case of an alcoholic who died, she finds that the building behind him has five other dead bodies. While investigating, she sees that part of the new police force is Tommy Sullivan, someone from her past 20 years ago. As the case goes deeper, they find not only that their victims are veterans, but also that they all had their spleens removed, prompting Megan to believe that a plastic surgeon is the one behind it. Kate has a meeting with a friend of hers and finds that he wants her to run for office; meanwhile, Tommy's partner Adam questions Tommy on what happened in his and Megan's past. After looking after a renowned plastic surgeon, they come across where he is killing his victims and Megan is forced to perform emergency surgery on the man they were using for 'bait' to catch the serial killer. After everyone believes that the case is over, Megan still questions what the doctor was putting in the bodies. Just as Megan is finding what was inserted in the body, she gets a call from Lacey's phone, only to find that someone has kidnapped her daughter.

Victims:

• Sergeant Vilmer Brazas
• Specialist Douglas Kessler
• Staff Sergeant Vincent Morgado
• Corporal Joel Moskowitz
• Corporal Caleb Witsman
• Doctor Harvey Wallace
• Alyssa Wallace
• Army Staff Sergeant Karl Simmons (Alive, but then blown up by selfmade bomb)

Murderers:

• Doctor Wallace
• Karl Simmons
• Nurse Yvonne Kurtz

After finding out that her daughter had been kidnapped, Megan tries to hide the fact that there is a bomb in the body of their victim, and that her daughter is missing. While Kate, Curtis, and Ethan begin realizing that something is off about Megan. Megan gets distraught when she is called on to the case of a teenage girl who was shot in the back, only to find that it was Dr. Wallace's daughter. As she goes to the man she just saved to see if he remembered anything, Tommy follows her, forcing her to tell him about Lacey's kidnapping. After meeting up with the kidnapper, and getting tazed, Megan awakes in a van with the very same man she just saved, only to find out that he, the doctor, and the doctor's head nurse Yvonne Kurtz (Annie Wersching), were involved in a plan to send a message out about wounded veterans. When Megan gets to her daughter, she finds that they are uninterested in the bomb, but they want Megan to implant the bomb in the man she had just saved. Tommy and his team barge into a building, thinking that Megan is in there, only to find that they took the tracking device out. Kate questions Ethan about why Megan is gone, only to realize that Megan has gone missing. After implanting the bomb, Megan plans an escape, only for it to fail. Just as Kurtz is about to shoot Megan, Tommy barges in and kills Kurtz.

Victims:

• Sergeant Vilmer Brazas
• Specialist Douglas Kessler
• Staff Sergeant Vincent Morgado
• Corporal Joel Moskowitz
• Corporal Caleb Witsman
• Doctor Harvey Wallace
• Alyssa Wallace
• Army Staff Sergeant Karl Simmons (Alive, but then blown up by selfmade bomb)

Murderers:

• Doctor Wallace
• Karl Simmons
• Nurse Yvonne Kurtz

Megan and Tommy are called onto the case of a young teenage girl who came into a clinic and broke her own arm, but Megan gets frustrated when everyone around her makes it sound like the young girl was possessed. Kate finds it hard to juggle campaigning and working her job; when Megan and Tommy go to the victim's house, they find both that the father is a very religious man, and that he strictly enforces it on his children. Megan and Tommy both suspect the father of having done it, but things change with another one of the daughters begin having the same symptoms. Curtis and Ethan get freaked out when they find crosses on the victim's body. Megan finds that the doctor who had worked on their victim was in a sexual relationship with her sister, who also stole PCP from him, meaning that she was poisoning her sister so that she could get more attention from her parents. Megan questions what she believes in when the sister tells her, "Quarter for your jacket, pumpkin?" This had been the same thing her father had told her.

Victims:

• Rebecca Banks
• Chelsea Banks

Murderers:

• Hannah Banks

Megan and Tommy investigate the case of a mob leader's son killed in a shooting, but when they arrive on the scene, they find that someone has now targeted them too, as they go under fire. The mob leader then proceeds to threaten Megan when he learns of his son's death. Tommy seems to have a past with the mob leader when he goes to his house. Megan finds that the child was not as innocent as everyone had believed him to be; he was beginning to get into the family business of selling drugs, but doing so on his own with the help of a former inmate and current gym owner who has supposedly gone straight. Megan gets angry with Tommy when he tells her she is no longer as spontaneous as she used to be, prompting her to go on a date with him, only to find that he had set up the date beforehand. When Megan, Tommy and Adam go to investigate a perpetrator, she finds the perfect way to be spontaneous. In a twisted turn of events, they find that the father had killed his son, in an effort to keep him from starting a competing drug business.

Victims:

• Nicholas Russo
• Jaxon Ware

Murderers:

• Daniel Russo

Megan and Tommy investigate two murders that seem to be the work of a vigilante. Megan uncovers a possible link through a grief counselor named Trent Marsh (Henry Ian Cusick). Kate prepares to announce that she's running for public office. Meanwhile, Megan's mother Joan is selling her house, and an upset Megan confronts her about a box of her father's items she found, including his suicide note. Megan asks Tommy to get the note's handwriting analyzed, as she refuses to believe that her father killed himself.

Victims:

• Freddie Delgado
• Lori Keyser

Murderers:

• Doctor Trent Marsh (arrested off screen)

Kate falls for a handsome and mysterious man named Sergei at a political event. A shocked Kate begins to have doubts about Sergei when a girl with connections to Ukrainian human trafficking ring is murdered near the hotel where Sergei is staying. Megan's autopsy reveals the girl was pregnant, and her baby had been removed via a crude C-section.

Victims:

• Oksana Svetlova

Murderers:

• Arco Starkovich
• Etta Starkovich

During a murder investigation, a man goes into a rage and bites Tommy. When a man in a similar state attacks a city bus patron, Megan turns to the new health commissioner Charlie Stafford (Luke Perry reprising his season 2 role), for help uncovering the truth behind strange rabies cases.

Victims:

• Melanie Summer (murdered)
• Seth Boylan - (infected transplant times 2)
• Norman Chen - (infected transplant)
• Brian Ellis - (harvested)
• Michael Finley - (harvested)
• Shawn Asher - (alive)

Murderers:

• Mason Geary

Megan finally accepts a date with Tommy. She leaves the dinner-bar rather than go home with Tommy, but reconsiders and goes back inside, only to find Tommy talking to a young woman. The next day, Megan arrives at the scene of the same young woman's murder, and finds Tommy covered in blood. As evidence piles up against Tommy, Megan tries to ignore her doubts and prove his innocence.

Victims:

• Jason Banning
• Skylar Green

Murderers:

• James Lawson

A wealthy fund manager (Christopher McDonald), on trial for defrauding investors out of a billion dollars, is kidnapped while leaving the courthouse and apparently murdered. During the kidnapping, a female protester outside the courthouse is run down by the getaway car, and her autopsy provides surprising clues. Megan gets closer to discovering the truth about her father.

Victims:

• Jennifer Sanchez

Murderers:

• John Anderson/ Doctor Colin Olsson
• Gerry Roberts

Joan refuses to let Megan have her father's body exhumed to examine. Shortly after, a schizophrenic teen is murdered at a mental institution. The institution's head doctor (Craig Bierko) comes under suspicion when he obstructs the investigation. Megan and Tommy are provided a clue by a young inmate named Darby (Hannah Leigh), who believes she was the intended target because the killer she witnessed is the same man that her mother hired to kill her younger sister years ago. When the mother (Sharon Lawrence) staunchly denies the accusations, Megan lets her feelings for the "silenced young girl" cloud her objectivity, and she takes the girl's side.

Victims:

• Renee Caldwell
• Beth Stone

Murderers:

• Darby Stone

When a plane crashes in Philadelphia due to a crazed U.S. Marshall opening fire while aloft, the entire team of Megan, Kate, Tommy, Adam, Curtis, Ethan, Riley and Stafford must go into disaster mode. Because the crash hit the city's main power grid, Megan must conduct autopsies on the victims during frequent blackouts. Things get further complicated when someone cuts the power feed in the building's backup generator and the body of one of the crash victims goes missing. Meanwhile, Tommy and Riley are in a serious car accident while trying to investigate the area where the plane's tail section landed.

Victims:

• Tom Westphall
• Air Marshall John Davies
• Carla Mendez

Murderers:

• Pam Jacks
• Air Marshall John Davies
• Alex Jacks

Note: Air Marshall John Davies was both the murderer and victim.

Robert Riley (Kenneth Mitchell), an inmate convicted of murdering his lover, violently escapes from a prison transport van and becomes a dangerous fugitive on the run in Philadelphia. He holds a list with names on it, including DA Russell, Megan, and two others. Soon another man turns up dead, and is revealed to be a witness who testified against Riley at trial. Megan must dig deeper into the original case (in which she herself presented evidence that incriminated Riley), when Riley corners her and insists that he is innocent and being framed. Suspicion begins to fall on Emmett Harrington (Alan Dale), a well-to-do area businessman who was married to the original murder victim, when evidence surfaces that two witnesses in the Riley trial received six-figure sums from Harrington's Cayman Islands account. When Megan gets the body of Harrington's former spouse exhumed, Kate finds something that Megan missed during the original autopsy.

Victims:

• Caroline Harrington
• Marcus Webb

Murderers:

• Stacey Harrington

Megan's father's exhumation is granted and she is shocked to find the coffin empty. Megan later finds a key that unlocks a secret compartment in her father's old study which holds a missing medical file for a young woman named Lindsay Pratt who was murdered the day before her father died by a serial killer named Earl Brown (Kurtwood Smith). Brown, however, denies killing Lindsay Pratt. Since he is already serving life for killing many others, he has no reason to lie. Megan and Tommy visit the retired detective who investigated the Earl Brown murders, Glenn Fitz (Jonathan Banks). He's positive Brown killed Lindsay, but Megan isn't so sure because Lindsay was killed in a different way. After Fitz is shot and Megan discovers that the recent dead body Kate is reconstructing was Fitz's former partner, Megan rushes to tell Tommy the news but instead finds Chief Martin. On a drive to the medical examiner's office, Chief Martin pulls out a gun revealing that she was the one who killed Lindsay Pratt (in a jealous rage). She also killed Megan's father and all the others to cover up any loose ends, and says that Megan is the only loose end left. Just as Chief Martin is about to shoot Megan, Trent Marsh steps in and shoots Chief Martin, saving Megan's life. In the end, Megan lets Tommy know that she's held the past against him for far too long, and they finally are together.

Victims:

• Doctor David Hunt - 35 years ago (Megan's Dad)
• Lindsay Pratt
• Detective Arthur Wilcox
• Detective Glenn Fitz
• Chief Angela Martin

Murderers:

• Chief Angela Martin
• Trent Marsh
• Earl Brown

Note: Chief Angela Martin killed Megan's dad 35 years ago before the pilot of the show. She was both the murderer for a long time and now a victim.