All That Remains is Patricia Cornwell's third installment in her Kay Scarpetta series. Scarpetta is working a case that involves the disappearance and murder of the daughter of the so-called Drug Czar, politician Pat Harvey. As Scarpetta investigates the case with her police counterpart and friend Pete Marino, she comes up against resistance from the FBI, which is attempting to hide information not only from the public but from Scarpetta herself. However, Scarpetta does not let this lack of cooperation keep her from continuing to attempt to do the right thing, which is to find the killer for Mrs. Harvey. All That Remains is a suspenseful novel that will keep the reader glued to the page until the last bullet flies.

Kay Scarpetta is about to settle down to a relaxing afternoon of gardening when she gets a call from police detective Pete Marino. Another abandoned vehicle has been found in a situation that resembles the previous disappearances of three couples. Scarpetta goes to the scene where she learns that the owner of the vehicle, Deborah Harvey, is the daughter of politician Pat Harvey. Scarpetta watches as the investigation begins. However, little information is gained from examining the vehicle, so the investigators must sit back and wait for Deborah and her boyfriend, Fred Cheney, to be found.

The next day, Pat Harvey calls Scarpetta to her home. Mrs. Harvey is aware of the past cases, the couple murders, and wants to know if Scarpetta believes this is what has happened to her daughter and her boyfriend. Scarpetta tries not to commit to anything, but does believe that this is the case. Mrs. Harvey picks up on what Scarpetta does not say and begins to take the investigation in her own hands. Mrs. Harvey calls in a psychic to help find her daughter's body while gathering information about the case through her political connections.

The following winter the bodies of Fred Cheney and Deborah Harvey are found in a remote clearing in the woods near the rest stop where the vehicle was found. When Scarpetta arrives, she finds that the bodies have been moved, something that is against the rules of investigation. Later, Scarpetta learns from a reporter friend of hers that a jack of hearts playing card is always found in the vehicles of these victims and this information makes her believe that this is most likely why the bodies were moved, in order for FBI agent Benton Wesley to look for the card before she arrived. Wesley later confirms this assumption.

Scarpetta performs autopsies on the remains and cannot determine the manner of death on either body. However, Scarpetta finds a bullet lodged in Deborah Harvey's spine. This is unusual because this killer has never used a gun with the other three couples. Shortly after making this discovery, Scarpetta decides to go back to the clearing and search for the bullet casing. Scarpetta finds the casing, but it turns out that it was planted by the police under orders from the FBI. The FBI had been hoping to lure out the killer with the planted evidence. However, their plans change when Pat Harvey throws a press conference. Mrs. Harvey openly accuses the FBI, the CIA, and the coroner's office of hiding information and of knowing the identity of the killer and hiding that as well.

Scarpetta changes the direction of her investigation into the case and begins searching through her files for cases that might be connected. Scarpetta finds two cases. One is the case of a dog shot three times by bullets similar to the one found in Deborah Harvey. The other is two women who were found murdered in a cemetery in Williamsburg under similar circumstances. Scarpetta and her friend, reporter Abby Turnbull, go to Williamsburg and are approached by a suspicious man. Scarpetta writes down the man's license plate, and this leads to the identity of a possible suspect. The suspect, Steven Spurrier, is placed under police surveillance. When Spurrier attempts to steal license plates from a car at the airport, he is placed under arrest and his house is searched.

Although the search does not find anything incriminating, the police are able to get a DNA sample to compare to blood found in the Harrison-Mott murders. While waiting for these results, Mrs. Harvey comes to Scarpetta and asks if she believes Spurrier is the man who killed her daughter. Scarpetta does not commit herself to a response, but Mrs. Harvey gets the answer she wants anyway. The next day, Scarpetta learns that Spurrier has been released from jail, that the DNA proved to be negative, and that Abby has gone to interview Spurrier. Scarpetta rushes to Spurrier's home to stop Abby only to arrive too late. Abby is dead, apparently shot by Spurrier, and Spurrier himself is also dead, shot by Pat Harvey. Mrs. Harvey comes into the room while Scarpetta is attempting to revive Abby and turns the gun on herself.