The Clue of the Black Keys is the twenty-eighth volume of the Nancy Drew Mystery Stories series.
Professor Terry Scott went to River Heights to ask the help of Carson Drew to help him to find Dr. Joshua Pitt. Mr. Drew thought that the case was more of a mystery, so he referred him to Nancy Drew, his daughter who loves detective work. Terry Scott and Dr. Joshua Pitt, together with their teammates, Dr. Anderson and Dr. Graham, found the clue to the treasure during their expedition in Mexico, a cipher carved in a stone tablet and three black keys. Before the professors had time to translate the cipher, the tablet disappeared together with Dr. Pitt, leaving only the bottom half of one of the keys. Terry suspected the Tinos because they vanished when the cipher stone and Dr. Pitt disappeared.
Someone tried to steal the half-key. Sergeant Malloy helped them identify the thief, Juarez Tino, but not until after he fled for Florida.
Terry gave the half-key to Nancy and that night a burglar broke into the Drews' house. A thief stole Terry's things and documents from the hotel room. Nancy asked her father's advice, and he suggests finding the other expedition members. Nancy and George meet with Dr. Graham, and he says the four expedition members trust one another. Ned Nickerson asks Nancy to drive his fraternity brother in Emerson College, Prof. Terence Scott, to his lecture. Bess and George trail Mr. Porterly, and overhear his telephone conversation planning harm to Nancy.
Dr. Anderson tells Nancy that Mr. Juarez Tino telephoned to say that he'd reveal where the cipher and Doctor Pitt are for a price. After Terry Scott's lecture, Mrs. Lillian Wagnell asked him to decipher her sea captain grandfather's old diary. Nancy doubts Mrs. Wagnell's intent, and Mrs. Prescott mentions that Mrs. Wagnell doesn't have a sea captain grandfather.
Mrs. Wagnell doesn’t want Terry to borrow the diary so Nancy suggests he take the important pages. Carson Drew received a letter from Caswell P. Breed in Baltimore, a relative of Dr. Pitt. The Drews went to Baltimore but Mr. Breed sent no letter. They guess that someone has lured them out of River Heights for some nefarious purpose.When Nancy came home she can’t contact Terry so she went to the Wagnells' house, only to find Terry imprisoned at their house. Terry discovered that the Wagnells and Porters were related to the stuepeds.
After those things happened, Terry went to Mexico and Nancy decided to join the educational trip of Dr. Anderson in the Florida Keys. A day before Nancy went to Florida, Juarez searched their house for the half-key, but couldn't find it.
When Nancy got to Florida she asked Dr. Anderson to work on a special assignment with Fran Oakes: to look for the Black Keys amongst the Florida Keys. Fran Oakes introduces Nancy to Jack Walker, her cousin. They went to Two Line Parker who knows about the Florida Keys history. The fisherman told her about the Black Falcon.
During their rest, Nancy found the burned letters in Porterlys’ place. There was an unburned part of letter that talked about her, and she concluded that the Porterlys had an evil plan for her.
Nancy and Dr. Anderson saw Juarez Tino in a speedboat while they were searching the Florida Keys looking for where the Black Falcon sunk. They tried to follow him but he lost them. Nancy decides to return there the next day. Dr. Anderson won’t allow her to go alone, but Terry joins her.
Nancy, Terry, Fran and Jack go to find the Black Falcon. They studied the Florida Keys and were found a hidden island where they found a hidden hut, where Dr Pitt was imprisoned. Jack and Fran called the police. Nancy and Terry stayed with Dr. Pitt until Mr. and Mrs. Juarez Tino, together with the Wagnells and Porterlys, arrived. They were able to get the half-key from Nancy. They asked Dr. Pitt to reveal the remaining clue and tell him that if he doesn't tell, something might happen to Nancy. He said that they can find the treasure in Mexico, in a little-known jungle region. They bring Dr. Pitt to Mexico and leave Nancy to their wives. The police arrived in time to free Nancy and Terry. They told Dr. Anderson that they must go to Mexico to follow the villain and rescue Dr. Pitt. They went to Mexico and captured the thieves. Dr. Pitt thought that they wouldn't be able to see the treasure, but Nancy helped them find it. The treasure belongs to Mexico and not to any of them.