The Dark Wind by Tony Hillerman is a story of narcotic traffickers operating in the Hopi Reservation area of central Arizona. The story unfolds with a covert drug delivery by a light aircraft to a remote dry wash in the Black Mesa area. The airplane crashes just near a vandalized windmill being staked out by Navajo Tribal Policemen, Jim Chee, who inevitably becomes involved in the Federal investigation into the missing cocaine. Chee has also been assigned cases involving the identity of a mutilated corpse of an unknown Navajo and the recovery of some pawned silver from the Burnt Water Trading Post. The trail of his unraveling of these seemingly unrelated cases takes him from interviews with traditional Hopi elders through the maze of the arroyos in the mesa country and to the Santa Fe State Penitentiary. The dramatic resolution of all the puzzles occurs in a violent thunderstorm during the secret rituals in a traditional Hopi pueblo.

The story begins with the discovery of the corpse of a dead Navajo by a party of three Hopis making preparations for their ceremony of the Niman Kachina. They delay reporting their find until after they have completed their ceremony. In the meantime, a Cessna aircraft crashes at night in Wepo Wash where Navajo Tribal Policeman Jim Chee is staking out a windmill, which is being repeatedly vandalized by persons unknown.

The plane is part of a cocaine delivery by drug traffickers. Besides the dead pilot and his passenger there is also another man at the scene who has been shot in the back. All traces of the drug shipment have vanished and Chee reports hearing a vehicle leaving the crash site. The DEA agent in charge of the investigation believes Chee is covering up his role in the operation and tries strong-arm tactics on Chee.

Along with his other assignments, such as reports of witchcraft on Black Mesa and the recovery of missing pawn silver from the Burnt Water Trading Post, Chee now has to contend with the suspicions of the unscrupulous and ruthless DEA agent and the fact that his suite of seemingly unrelated cases seem to be inextricably bound up together.

Fortunately for Chee, he has made friends with Cowboy Dashee, a Deputy Sheriff from Coconino County, who is also an adherent to the traditional Hopi ways. Together they gain the cooperation of Hopi elders, one who actually found the unidentified corpse, and the other who was in Wepo Wash on the night of the crash. Chee supplements the information from the Hopi elders with the results of a visit to the Santa Fe State Penitentiary and eventually comes to the conclusion that he understands the sequence of events that binds all these puzzles together. He unearths the missing cocaine and goes to where he has learned the hijacked shipment will be returned to the dealers.

In a dramatic sequence of actions, during the secret Hopi rituals in a village below the rim of the mesa, Chee confronts the murderer of the unidentified Navajo, the instigator of the plane crash, and the hijacker of the cocaine. They are all the same man, Jake West, the operator of the Trading Post, and his motivation is to avenge the murder of his son in the Santa Fe prison. Before Chee can arrest him, the DEA agent intervenes and tries to make off with the cocaine shipment. He plans on shooting Chee in the process. He is forestalled by Jake West who, despite being shot by the DEA agent, manages to propel him into the torrential waters of the flooding river. Chee is told the final answers to the mystery by the dying West and then, still handcuffed, Chee pushes the cocaine shipment into the flood waters. He thus gets rid of any evidence that he was ever involved in the Federal investigation.