Eyes of Prey is the third in the Prey series by bestselling author John Sandford. In this novel, Lucas Davenport is still reeling from the depression his last case left him with. To draw him out of this funk, Lucas's commander puts him on a case investigating the death of Stephanie Bekker, the wife of a pathologist thought to be involved in her death somehow. As Lucas becomes engrossed in the case, he finds himself drawn to a witness who has had the same experiences with depression. When this witness becomes the target of the killer, Lucas has more to lose than just a case. Eyes of Prey is another fast paced crime drama that pits Lucas against two criminals that will have him fighting for his own sanity.

Carlo Druze breaks into the home of Stephanie Bekker and kills her exactly as her husband instructed him to do. However, neither Druze nor Stephanie's husband, Michael Bekker, expected that she would not be alone. In the upstairs bathroom is Stephanie's lover. The lover comes downstairs and sees the killer. Shocked, the man runs away, giving Druze time to escape. The lover checks on Stephanie, decides she must be dead, and rushes back upstairs to dress. The lover erases all evidence of himself from Stephanie's home, leaves, and calls the police from a pay phone. Stephanie, however, was not dead. Stephanie struggles to reach the phone, but dies just inches from it.

Del, a narcotics officer and friend of Lucas Davenport, tells Lucas about the death of his cousin, Stephanie Bekker. Del would like Lucas to look into the case. Lucas resists, but is not able to give Del a definite answer because the pimp they are waiting for walks into the bar. The pimp pulls a knife when Lucas moves to arrest him, so Lucas beats him up, fueled by his anger at what the pimp did to Lucas's snitch. The following morning, Lucas learns that he will have to face an internal affairs interview for the beating.

Lucas's commander, Quentin Daniel, knows that Lucas has been suffering depression since his last case in which a suspect broke into his home and injured his infant daughter. Lucas assigns Lucas to the Bekker case, hoping the investigation will help draw him out of his depression. Lucas begins by investigating the husband, Michael Bekker, a pathologist at the local university who has a reputation of being obsessed with people who are dying. Bekker once worked on the oncology ward in the hopes of helping develop better ways of dealing with impending death. One of the oncologist tells Lucas he believes Bekker might have been involved in the deaths of one, maybe even two, of the patients. However, the doctor cannot prove anything, so charges were never brought against Bekker.

Bekker is aware that the police believe he is involved in his wife's death. Bekker does his best to pretend to be the grieving husband, but is anxious to move on. Bekker wants to sell the house Stephanie loved so much and buy a smaller condo, someplace more modern and luxurious. In the meantime, Bekker tries to minimize contact with Druze. However, Bekker has promised Druze he will kill Druze's boss, Elizabeth Armistead, in payment for Druze's killing Stephanie. They have planned it out carefully. However, Bekker strays from the plan by killing Armistead earlier than planned.

At the house of Elizabeth Armistead, Lucas comes to investigate the murder. Lucas is introduced to Cassie Lasch, the woman who found the body. After their brief conversation, Lucas speaks to a neighbor. As Lucas leaves, he runs into a reporter who wants to make a deal with Lucas. The reporter wants advance information about the case in exchange for a favor. Lucas agrees and tells her that he believes the same person who killed Bekker killed Armistead.

Lucas convinces his boss, Quentin Daniel, to use the newspaper to convince Stephanie's lover, whom they have dubbed Loverboy, to give them more information beyond the letter he has already sent. There is a press conference and Lucas attends. Afterward, Lucas runs into his ex-lover, Jennifer. Lucas tells her he wants her to decide if they should continue their relationship and let him know what she thinks.

The following day, Lucas goes to the theater where Armistead worked and runs into Cassie. Cassie helps Lucas find the name of a person who called looking for free tickets from Armistead for the previous night's performance. Lucas calls the person and learns he was out of the country the night before and could not have called. Then, as Lucas and Cassie talk, Lucas sees an actor on stage. Cassie tells him it is Carlo Druze, one of the theater actors practicing a part of their current play. Cassie tells him Druze was in the theater all night the night before.

Lucas and his team receive a picture from Loverboy that appears to be a copy from an art book or calendar. The picture is Redon's Cyclops. Lucas takes a copy of this picture and tries to find out where Loverboy might have gotten it from. About the same time, Cassie calls Lucas. Lucas thinks about brushing her off, but instead he calls her back. They become lovers. Cassie tells Lucas that she once battled depression too. When Cassie shares her story with Lucas it helps him feel less insane.

Bekker is concerned about Stephanie's lover. Bekker does not want Loverboy to come forward and point fingers at Druze, who might then turn on Bekker. Bekker searches through Stephanie's things, making Druze look at hundreds of photographs in hopes of recognizing Loverboy. When this does not help, Bekker begins looking through Stephanie's personal papers. Eventually Bekker finds phone calls between Stephanie and a man named Philip George. George fits the description Druze gave to Bekker of Loverboy. Bekker tells Druze he has to kill George.

Druze, unhappy with the idea of committing a murder that was not part of the plan, flattens one of George's tires and waits for him in the parking lot of the university. When George comes out, Druze kills him with a blow to the head, then places him in his own car and drives him to an empty cabin, where he buries him in a marshy area beside a lake. Druze forgets to cut George's eyes as Bekker told him to do. However, Bekker knows that Druze has made this mistake when he has a hallucination in which George turns into a snake and stares at him. Bekker insists that he and Druze return to the burial site and destroy George's eyes. They return and leave safely, unaware that a woman in an adjoining property has seen them.

Lucas goes to the site of George's burial and watches as the local cops recover George's body. When Lucas sees George's eyes, he knows that the same man who killed Bekker and Armistead killed George. However, when Lucas visits the home of George's wife, he realizes that George could not possibly be Loverboy. George knew nothing about art and he had a much higher voice than the man who made the 911 call. Lucas talks Daniel into allowing him to make another public appeal to Loverboy.

In the middle of the night, Lucas receives a call from a man claiming to be a doctor treating his daughter. Lucas takes the call and discovers that it is not a doctor, but rather Loverboy. Loverboy tells Lucas that he cannot come forward but that he wants to help. Loverboy gives Lucas a few more details about the killer and urges him to continue working on the case. Loverboy and Lucas arrange a way in which Lucas can alert Loverboy that he needs to hear from him again. Not long afterward, another woman is murdered.

Bekker convinces Druze that they need to kill another woman to make it look as though a serial killer is on the loose. Bekker tells Druze to pick a woman at random at a mall. Druze does, leaving the woman in her car in the mall parking lot. A young boy sees the murder, not aware of what he is seeing, and goes to the car to see what the woman is doing. The boy reports the murder and Lucas talks to him. The boy tells Lucas to watch a movie called Darkman. That night, Lucas watches the movie with Cassie. Cassie tells him that the Cyclops and the man in Darkman both resemble Carlo Druze.

Lucas puts out word to Loverboy that he needs to speak to him. While waiting for a response, Lucas continues to investigate. At the hospital connected with the university where Bekker works, Lucas is told that Bekker has been harassing an ALS patient, holding her nose closed so that she cannot breath in order to watch her eyes in the moment of death. Lucas has the woman interviewed on tape. Lucas then arranges to have the bodies of the two cancer patients exhumed so that he can see if their eyes were cut. Lucas believes this is the best way to prove Bekker killed these children.

As Lucas is investigating, Bekker turns his attention to Cassie. Cassie has been seeing Lucas and Bekker is afraid she will identify Druze as the killer. Bekker ties Cassie up in her apartment and then brings Druze to see her. While Druze is attempting to speak to Cassie, Bekker shoots him in the head. Bekker then slices Cassie's throat. Lucas goes to Cassie's apartment with Sloan to check on her and they find the bodies. Lucas is devastated and has to be sedated.

The following day, Lucas puts all his energies into proving Bekker's guilt. After the exhumation proves that Bekker killed the two cancer patients, Lucas sets up a sting at the funeral parlor where Druze's body is. After Bekker comes in and cuts Druze's eyes, Lucas and his team announce their intention to arrest him. Del punches Bekker in revenge for his cousin's murder. Lucas then takes the sight on his gun and beats Bekker so badly on his face that he will forever be disfigured. The following day, Daniel tells Lucas he has so many complaints pending in internal affairs that he could face charges. Daniel suggests Lucas retire. Lucas does, but leaves behind a list of clues that suggest the identity of Loverboy. Loverboy is Daniel.