Megan returns to work months after Peter's death, and she is surprised by a man from her past - Tommy Sullivan, the new detective assigned to her case. Megan, along with Tommy and his rookie partner, Adam Schaeffer, must stop a serial killer whose victims are young war veterans. As she learns more about the crime, the stakes rise when she gets a call from the killer -- who is holding her teenage daughter, Lacey, hostage.
In conclusion of the thrilling Season 3 premiere of Body of Proof, Megan learns why a serial killer targeted war veterans and just how one of their prime suspects figures in the case. But the killer has kidnapped Megan's daughter and is making sure that, now that Megan has cracked the case, she cannot reveal the answers to her team or the police while Lacey's life hangs in the balance. Meanwhile, Kate comes under fire with District Attorney Dan Russell.
Megan and Tommy investigate a murder that appears on the surface to be a case of severe child abuse. But the girl's parents, Caleb and Laura Banks, claim that their daughter was killed by the Devil after being possessed. The team must try to separate fact from fiction when the victim's mother begs Megan to help her stop the same thing from happening to their surviving daughter.
When the son of a New York mob boss is found shot to death in an alley, Tommy, Adam and Megan investigate, only to be shot at themselves. Back in the morgue, the mobster threatens that he will make sure whoever killed his son won't live to see another sunrise. When an early suspect is gunned down, Megan and her team realize they have to solve the case before more bodies pile up.
Megan and Tommy must solve two murders that appear to be the work of vigilante killer. After Megan questions Trent Marsh, the grief counselor for one of the victim's parents, she decides to take him up on his offer of counseling her on her own issues about her father's suicide. But Megan is shocked by what she finds in his waiting room.
Kate meets Sergei, a handsome and mysterious guest at a political event, and is irresistibly drawn to him. But when a young Russian girl is found murdered near the hotel where she and Sergei are having a tryst, Kate begins to suspect that he may be involved and turns to Megan for help.
Megan and Tommy investigate the savage murder of a young woman, which leads them to her neighbor, who bites Tommy and is diagnosed with rabies. When another rabies fatality comes in without any bite marks, Kate calls in the new health commissioner, Dr. Charles Stafford, to help Megan uncover the truth. Could it really be zombies, as some of her colleagues suspect?
A young girl is found murdered, and when Megan arrives at the scene, she finds Tommy covered in blood. As the evidence piles up against him, Tommy claims he cannot remember what happened the previous night. Though Megan has doubts about Tommy's involvement, she's the only friend he has in this situation and has to put her personal doubt aside to try to prove his innocence.
A rich investment fund manager, Gerry Roberts, stands trial for defrauding his investors of a billion dollars, but he is kidnapped as he is leaving court, even though Tommy and Adam are on his security detail. In all the chaos, a protestor outside the courthouse is run over and killed by the getaway car, and later a video surfaces of Gerry being killed. But was it possible he faked his own death? Megan also gets closer to the truth about her father.
A schizophrenic teenage girl at a mental institution is found murdered. When Megan and Tommy interview a young patient named Darby, who seems extremely sane and lucid, she tells them that she saw the killer climb down from a heating vent in the ceiling, but most shocking of all -- he meant to kill her, not the actual victim. Could the killer be Dr. Malcolm, the ward director, who is obstructing their investigation
When a plane crashes in Philadelphia due to a gunman opening fire while aloft, the entire team of Megan, Kate, Tommy, Adam, Curtis, Ethan, Riley and Stafford must go into disaster mode. Since the crash hits the city's main power grid, Megan must conduct autopsies on the victims during frequent blackouts, but then one of the bodies goes missing. Meanwhile, Tommy and Adam are in a serious car accident while trying to investigate.
An inmate violently escapes from a prison transport van and becomes a dangerous fugitive on the run in Philadelphia. Soon another man turns up dead - who's revealed to be a witness in the escaped prisoner's murder trial. Megan must continue to search for the truth in the original case when the accused murderer shows up and pleads with her that he is innocent and being framed.
Megan probes more deeply into her father's suicide so much that she finally gets some closure.