Something creepy is happening. A man is duct taped to a chair as an intruder with a knife terrorizes his wife.
Cut to Jane Rizzoli (Angie Harmon) playing basketball with her brother Frankie (Jordan Bridges). She takes an elbow to the nose. Their mom (Lorraine Bracco) comes in to see the blood and gives her grief for rough-housing with her brother. Rizzoli is called away to the murder scene.
At the scene, coroner Maura Isles arrives. Rizzoli arrives and trumps Detective Crow for the case. A young detective named Frost loses his lunch nearby. He warns her it might bring back memories.
Inside, Rizzoli runs into her former partner Det. Korsak (Bruce McGill). He warns her it's bad.
They find the husband posed on the couch, with his throat precisely slit. His wife Gail is missing. There's a tea cup on the floor.
Flash back to Rizzoli going into a basement to rescue a woman and getting cracked on the head. She asks if "the Surgeon" is out of prison. Although he's not, the victim was killed according to his MO, complete with a stun gun mark -- a detail they never released to the public.
They're joined by FBI Agent Gabriel Dean. He says he's there to observe, but Jane gets territorial. They find evidence that the suspect raped the wife and made the husband watch, just like "the Surgeon," Hoyt.
Jane and Frost go to visit him in prison. She asks whom he taught. He wants to see her hands. He asks if they still work. Flash back to him leaning over her unconscious body and stabbing scalpels through her hands.
He gets up to leave until she admits she does dream about him. Hoyt says his friend is out there.
Rizzoli gets a call that Gail Jaeger has been found. At the scene, the FBI guy Dean is there with the homicide detective. Isles says Gail has been dead 36 hours. She's naked (with foliage in all the right places) and laid out serenely.
At the autopsy, Dean and Korsak join them. At Dean's suggestion, Isles finds evidence of necrophilia.
Hoyt hears guards coming for him in his cell and takes a pill he has stashed. He goes into convulsions.
Dean joins Rizzoli and Isles and tells them that Hoyt escaped. He ingested something to fake appendicitis then attacked the doctors.
Back at her place, Rizzoli shooes her brother and Frost away. Her neighbor Marissa drops by later when she notices Jane doing her late night "nervous vacuuming." They're interrupted by her mother, who tells Jane her dad is also in the car outside with Frankie. She gives Jane grief for being a cop and for her brother wanting to follow in her footsteps.
Jane goes to Maura's house. She watches her feed strawberries to her giant tortoise. The doorbell rings.
Maura claims someone is dropping something off, even though it's the middle of the night. It's Dean with a file. He leaves.
Maura tells Jane that Dean wanted her opinion on a case, but she can't talk about it. Maura thinks somebody should date Dean.
"Should we draw straws?" Maura asks.
"Shouldn't we just show him our tits and let him decide?" Rizzoli asks.
Later, she admits she's never been so scared in her life.
The next day at work, Rizzoli tells Korsak to give Frost a break. He's bitter they're not still partners. He apologizes for not warning her that the crime scene looked like that of "the Surgeon."
She gets a call about another victim. They find the man duct taped to a chair. No tea cup, which means he didn't need a warning device because Hoyt was with him. The man's wife is missing.
A flower delivery comes for Jane. The card says: "Prickly on the outside, succulent on the inside, just like you. Best -- Henry Deduboto," an anagram for Theodore Bundy, they deduce. Frost calls. They found the next wife.
Rizzoli warns Isles she won't like her plan. They go check out the body, in a remote wooded area. Jane tells Maura she wants to leave the body and wait for the suspects to show. She thinks they had to kill again because the cops found the first body so quickly.
They stake out the scene. Jane isn't thrilled about the stinky mutt Korsak picked up for her and named "Jo Friday." He gets out of the car to pee but doesn't immediately come back. Jane goes to investigate. She sees someone running away. She tackles him, but it's Dean. He was chasing Hoyt.
They find Korsak nearby with his throat cut. He's barely conscious.
Jane visits Maura, who confesses she told Dean where they were.
Later, Dean knocks at Rizzoli's door. She has brought Korsak's dog home. She invites him in for coffee after choking out an apology for tackling him.
Dean asks why Hoyt came after her. She says Hoyt's first victim was her case. He asks about her hands. She tells him about when Hoyt had her pinned to the floor with a scalpel to her throat. Flashback to Korsak coming in and shooting Hoyt and saving Jane from further injury or death.
Dean offers to stay, but she declines. The next day at work, Rizzoli dodges her mother's calls. Isles tells her she's going to Quantico tomorrow and that the case is bigger and more complicated than they thought. She says she's been ordered not to tell Jane about it and it involves national security.
Rizzoli storms into the FBI, demanding answers. She runs into a U.S. Senator. He shows her photos from Afghanistan of similar crime scenes. Their working hypothesis is that Hoyt's apprentice is a soldier. He's not in the databases because he was a Green Beret working for the CIA, who had his ID wiped.
Rizzoli remembers that Hoyt used an assumed name to get into a medic training program at Fort Stewart. Dean suggests they fly there in the morning.
He asks if she wants to get dinner but is called away. Maura calls Jane to tell her her apartment has been trashed.
Dean calls her to tell her the apprentice is John Stark, a medical care specialist. He has the address. Outside her apartment, a paramedic stops Jane and asks her to ID the body. What body? He tells her it's her neighbor. She climbs into the van and finds Hoyt waiting for her in a body bag. The paramedic is Stark, the apprentice. They knock her out.
She comes to, tied up on the floor of the van, with Hoyt holding her gun. He drags a scalpel across her neck, drawing a few drops of blood.
Stark calls Hoyt outside, and Rizzoli frantically looks around the van for a weapon or a way to get free. She finds the roadside emergency kit and grabs something as she collapses and feigns unconsciousness. Hoyt peers over her, and she rolls over and sticks a road flare in his eye. She grabs his taser and rolls out of the van, still duct-taped up then zaps him until lit won't zap anymore. She waits for it to recharge as Stark comes running. She zaps him, too, and he drops his gun. She grabs it and shoots him twice. She looks around for a way to free herself while keeping an eye on both men. She finds a scalpel and is using it to saw at the duct tape as Hoyt reaches for the gun.
But she's free and steps on his arm. She picks up the gun and stands over him. She fires. "We match," she tells him as we see that she has shot a hole through his hand.
Later, Dean joins her and says the apprentice was a decorated soldier. He asks her out. She tells him she just wants to go home, but says "thanks".
He arrives home and finally sees her trashed apartment. "Jo Friday" joins her, followed by Maura, bearing tiny tortoises. She's there to help clean, in designer duds.
But Jane suggests Bloody Marys instead.