Violets are Blue continues the story of Washington DC police detective Alex Cross. In the opening chapter, Cross arrives at the murder scene of his partner and lover, Betsey Cavalierre. Before he finishes examining the scene, he receives a call from his nemesis, the Mastermind. Though the Mastermind has plagued and taunted Cross for some time, he continues to evade the authorities. After threatening the safety of Cross's family, the Mastermind vows that Cross will be his next victim.

The story then jumps to San Fransisco, where two young soldiers jog through Golden Gate Park. From out of nowhere, a tiger attacks the male soldier. When his female friend attempts to flag down help, two men attack her, biting and beating her savagely. They tell her she has been chosen. Kyle Craig, a detective with the FBI, calls Alex Cross into the case as it bares a resemblance to a case Cross worked in DC, where the killers hung their victim and drained her blood. When the police learn the characteristics of the murders, they begin an investigation into the strange underworld of practicing vampires.

Cross interviews various experts on vampire culture, such as the Fresno Kid, a man who fits vampires with dental extensions, in other words, fangs. The bite marks of the killers match those of someone with extended fangs. Cross also meets vampire expert Peter Westin at the University of California. Westin gives Cross a description of a real life vampire, as opposed to a role playing vampire. When Cross leaves his meeting in Westin, he believes in vampires a little more.

Despite multiple murders and countless man hours, leads in California dry up. Frustrated, Cross returns home. After spending some time catching up with his family and work, he receives another call from Craig. Another vampire style murder occurred in South Carolina. Even while Cross and Craig investigate the crime in South Carolina, news breaks of another murder, this time in Charlotte, North Carolina. There police apprehend a number of young people living in a vampire commune. One young man, Irwin, confesses to killing his parents. Authorities, however, clear him of the other current murders. Before the questioning ends, Irwin bites Cross. The wounds become infected, and Cross's recovery restricts him to home. There, he uncovers a link between the locations of the murders and a traveling magician's show. The FBI quickly moves to the next stop on the show, New Orleans. Cross rejoins them as soon as the doctor clears him to return to work.

It quickly becomes clear that the magicians, Daniel and Charles, practice a vampire lifestyle. Cross and Jamilla Hughes, detectives from San Fransisco, attend a fetish ball at the magicians' home. There, Charles identifies himself as The Sire, a ringleader among vampires. However, just as he introduces two new vampire princes, the lights go out. When they come back on, the two princes lie dead. Further searches of the house reveal the dead bodies of the magicians, as well.

It appears that the investigation dies again, until Hughes uncovers a lead to the vampire capital of the world: Santa Cruz, California. When she drives there to investigate on her own, against Cross's advice, two men, also brothers, abduct her. The two brothers, William and Michael Alexander, practice the vampire lifestyle. Through their eyes, the readers witness many of the murders that Cross and Hughes are investigating. They take Hughes to the farm where they grew up and where a large society of vampires now reside.

When he cannot contact Hughes, Cross becomes worried. He learns of her solo trip to Santa Cruz and immediately flies back to California, alerting Craig to the situation. The FBI surrounds the farm and watches it all night while gaining intelligence on the inhabitants. The next morning, as the authorities approach the farm house, the vampires appear in pairs, in dark, hooded robes. When Hughes falls to the ground, Cross recognizes her and signals for a sniper to kill the man guarding her. As the agents apprehend those outside, Cross moves into the house in search of the Alexander brothers.

Cross finds an entrance to a long tunnel from inside the house. He enters it, only to find that the Alexander's pet tiger resides deep inside the tunnel. When Craig enters the tunnel behind him, Cross issues a warning. As the cat approaches, Cross fires several times, finally killing the tiger before it kills either agent. Hughes, Craig and Cross make their way to the end of the tunnel. They find themselves in a large cave. Suddenly, a truck bares down on them. Inside, they identify the Alexander brothers. Cross holds his ground as he fires. Even when the truck backs up and charges again, Cross continues to fire. The truck flips and rolls through the field. In a rage, Michael emerges. Craig fires one shot and stops Michael short of attacking Cross.

Cross approaches the truck when he spots more movement. Inside he finds a dead William Cross and a living and still arrogant Peter Westin.

The cops begin to piece together the vampire case. Westin met the magicians some time back. When he felt strong enough to oust them, he instructed the Alexander brothers in murdering along the show's route. With the death of Charles, Westin assumed the role of The Sire.

Cross feels victorious in solving the vampire murders, but unease follows when he remembers the Mastermind is at large. Instead of leaving California, he takes up watch outside of Jamilla Hughes's house in San Fransisco. The Mastermind calls, taunting, threatening Cross's family in Washington DC. Just as Cross begins to doubt the wisdom of his decision, he spots the Mastermind on Hughes's street.

Cross shockingly realizes that Kyle Craig is the Mastermind. In a frenzy, he calls Hughes, sharing the news with her. She instructs him to enter her house and the two watch for Craig all night, to no avail. The next day, Cross shares his discovery with the FBI. FBI director Burns shares evidence that supports Cross's claims. Cross arranges for the safety of his family and begins the pursuit of Kyle Craig.

The hunt for the Mastermind, aka Craig, leads Cross back to Washington, where Craig kills Cross's friend at the Washington Post, Taylor and his wife. Cross then moves to North Carolina, where he fears Craig will attack Kate McTiernan, a former victim of the Casanova serial killer. Cross sets himself up in McTiernan's home in Nags Head. Once there, Craig bursts from the attic. During the ensuing altercation, Craig stabs Cross with an ice pick, but Cross recovers and knocks Craig unconscious. Cross then places a call to his home answering machine. This allows him to record the following conversation with Craig in which Craig confesses to, among other things, killing Betsey Cavalierre.

Cross finally ends the novel at home with his family, recovering from the stabbing. He rests in the peacefulness of his life, as he plays the piano on his sun porch. No one brings news of a murder, vampires or crooked cops. Cross also relaxes due to his decision to resign from the Washington DC Police Department.