In the opening of the 1929 edition: Frank is 16, and Joe is 15. Frank and Joe Hardy enjoy a relaxing Saturday afternoon boating with their friends Biff Hooper and Tony Prito. They rescue Evangeline Todd. There was a fire and explosion on the boat that the crew was eventually able to contain. The boys discover that she is on her way to see their dad, a well-known private investigator.
Evengeline goes to the Hardy house and tells them her story. Four months ago, after she and her brother, Professor Todham Todd, had been injured in a train wreck, he disappeared the night before their case against the railroad company was to go to trial. Evengeline asks Mr. Hardy for help in finding her brother, and he takes the case. Mr. Hardy goes to the Todds' hometown to search for clues and discovers that people have seen Professor Todham Todd. However, the professor doesn't stay in one place very long and seems to have lost his memory.
While Mr. Hardy is gone, Evengeline Todd tells Frank and Joe that Todham's shoelaces are always untied and that he often says the phrase "by jing." When school is out for the summer, Frank and Joe decide to explore the caves on the coast with their friends Chet Morton and Biff. Their friend Tony is unable to go with them. They travel by motorbikes.
On their way, they stop for a swim break, and Frank's motorcycle is stolen. They chase the thief and don't catch him, but eventually do get the motorcycle back. The boys stay in a hotel overnight and finish the ride to the Honeycomb Caves the next morning. They stop at a general store in the area.
In the opening of the 1992 edition: Frank is 18, and Joe is 17. In the Hardys' front yard, Frank and Joe are talking to their friend Chet as he uses a metal detector to look for treasure; Biff joins them. Biff suggests looking for treasure at the Honeycomb Caves. When Mr. Hardy gets home from work, he asks Frank and Joe to help him with a case on Telescope Hill. The U.S. government is setting up a radar station on the coast, and there have been some problems they want Mr. Hardy to investigate. Mr. Hardy suspects an inside job.
Later, Mary Todd arrives and wants to talk to Mr. Hardy, who knew Mary Todd's dad. Mary Todd's parents have died, and her brother, Professor Morgan Thomas Todd, has disappeared. Morgan Thomas Todd taught foreign affairs at Kenworthy College and disappeared several days before the summer break. Mr. Hardy decides to take this case, too, and Frank and Joe agree to help. Chet's sister, Iola Morton, comes by and offers to let Mary Todd stay with the Mortons. Frank and Joe tell Biff and Chet that they won't be going to Honeycomb Caves.
After dinner, Mr. Hardy, Frank and Joe go to Telescope Hill. As they are leaving, someone comes out of the bushes and jumps over the fence. Frank finds a cap hanging on a bush. The next morning, Frank and Joe leave for Kenworthy. On the way, they get into an accident. The truck driver tells Frank and Joe that there have been other accidents involving vehicles going to and from Telescope Mountain. Arriving in Kenworthy, the boys check into a local motel and then go to the college to start investigating.
Later that night at their motel, the boys are ambushed in their room and then taken outside and tied to old railway tracks. The boys escape, discover who was behind it and confront them. Frank and Joe then decide to search Morgan Thomas Todd's office before they leave campus. After they find a clue in an exam paper, they go back to their hotel.
When Biff and Chet arrive, the Hardy boys tell them about the recent events. The four friends decide to follow up on the clue together and go to Rockaway. Frank and Joe get a call from Mr. Hardy, though, and need to return to Bayport. Chet and Biff go on to Rockaway and Honeycomb Caves. In Bayport, Frank and Joe meet their dad at the radar site where he is investigating a downed tower.
Later, a report comes in on Cadmus Quill, Morgan Thomas Todd's colleague. Frank asks the chief of police in Kenworthy to interview Cadmus Quill. The chief calls back with news that Cadmus Quill has disappeared. As the boys get ready to pack the car to look for Cadmus Quill, Chet calls. He tells the Hardys that Cadmus Quill has followed him and Biff from the college and has almost run them off the road on the way to Rockaway. Chet asks Frank and Joe if they want to meet him and Biff. As the boys are leaving, their mom tells them that their aunt, Gertrude Hardy, is coming for a visit and asks the boys to pick up a spinning wheel for their aunt at an antique shop near Rockaway. The boys stop at a general store in Rockaway.
Both editions converge at this point in the plot: A gentleman at the general store warns them about strange things — lights and shooting — that have happened at the caves. The four friends decide to continue on to the caves anyway. When they realize that they can only access the caves by water, they ask a local fisherman if they might store their motorbikes (1992 edition: park their car) at his cottage. The fisherman agrees, but also tells them that he has seen lights and heard strange noises — shooting and screaming.
A storm breaks out while the boys are hiking to the ravine. Joe loses his footing and goes over the side of a cliff. After Frank, Chet and Biff find Joe and pull him up to safety, the friends continue their trek. Once the boys reach the ravine and the entrance to one of the caves, they make camp inside the cave for the night. While they are sleeping, someone else comes in. Joe hears the intruder and wakes the others up. The friends discover lots of tunnels and other caves in their subsequent search, but no intruder. While searching, the boys get separated, and Frank falls into a pit (1992 edition: Biff falls into the pit). When the three friends return to the cave to light a fire, they discover that some of their provisions are missing. After building the fire, Joe and his friends rescue their friend in the pit (1929 edition: Frank calls out from pit. The boys hear his voice. 1992 edition: Biff reaches his hand out of the pit, and the boys see his hand. Chet brings his metal detector on the trip, and finds a gun with the instrument. As the four boys explore the beach, they find another cave, and this one has a person living in it.
In the 1929 edition: Captain Royal, as he calls himself, is initially friendly to the boys but then asks them to leave the cave. The boys spend the rest of the day swimming and exploring. That night in their cave after Biff and Chet are asleep, Frank and Joe recall Captain Royal's use of the phrase "by jing" and his untied shoelace. They wonder if Captain Royal is the missing Professor Todham Todd. The next morning, the boys split up — Chet and Biff fish, and Frank and Joe return to Captain Royal's cave.
In the 1992 edition: The character's name is Commander E.K.T. Wilson and he doesn't have untied shoelaces or say "by jing." The four boys decide to look for some food after they leave the cave. As they walk along the beach, Chet takes out his metal detector and discovers the boys' stolen supplies buried in the sand. After they prepare the food, the boys split up. Chet and Biff go to the cliffs to fish; Frank and Joe return to Commander Wilson's cave. The brothers ask Commander Wilson if he has seen Morgan Thomas Todd or Cadmus Quill. Commander Wilson initially says no, and then he tells Frank and Joe a story about a second mate named Todd. After the boys leave the cave, Frank tells Joe he saw a cap in Commander Wilson's cave that looked like the one they saw at the radar site. When Frank and Joe see the Commander exit his cave a little while later, they decide to go back to the cave. There they find a codebook.
The following scene is only in the 1929 edition: On the way to Captain Royal's cave, Frank and Joe see someone lying drunk on the beach. As they get closer, they discover it is Carl Schaum, a car thief from their last case, who had escaped from jail. The boys think Carl Schaum was the person who stole Frank's motorcycle and their provisions. Frank and Joe tie up Carl Schaum and then throw cold water on him to wake him up. After the Hardy boys find someone to take him back to Bayport and the police, they go back to the caves. First, to Carl Schaum's to look for their provisions, then to Captain Royal's cave.
Ending for the 1929 edition: While the boys are in the cave, Captain Royal returns and is angry that they are looking through his stuff. He grabs the boys and a skirmish ensues. Captain Royal is able to get to his shotgun and aims it at the boys. Joe creates a distraction, but Frank is unable to escape. Hearing a gunshot, Joe runs back for his brother. Frank is fine. The shotgun was loaded with white flour. When Captain Royal leaves the cave and climbs up the cliff to escape the "enemies," he slips and falls into the water. Frank rescues him. The boys are able to get help to take Captain Royal back to Bayport to see the doctor. The next morning Mr. Hardy goes to visit Captain Royal in the hospital. Evengeline comes back to Bayport and says it is her brother. Todham Todd does not regain complete consciousness for a few weeks, and when he does he doesn't remember anything about the time after the railroad accident — including living on the beach as Captain Royal. Evengeline asks the Hardys and their friends not to tell her brother about that time. When Frank and Joe will not take a reward from Evengeline, she decides to give them and their friends a banquet to say thank you. At the banquet Evengeline gives Frank and Joe motion picture cameras; Biff and Chet each get a gold watch and chain. Todham Todd goes back to his work as a college professor.
Ending for the 1992 edition: Commander Wilson discovers the boys searching his cave. He gets his shotgun and aims as the boys run out of the cave. He fires the shotgun — and Frank is hit with an explosion of white flour. The two brothers manage to get out of the cave and down the beach toward the water. Commander Wilson goes to the mouth of the cave. From a distance, Frank asks Commander Wilson where he got the hat. Commander Wilson says he got it in Rockaway. The boys head back to their cave. Chet and Biff come back from fishing; they tell Joe that Chet discovered a mine at the top of the cliff. The four friends go back to investigate and pick up a straight line to the Palais Paris restaurant with the metal detector. When they dig, however, they don't find anything. The boys decide to go back to Rockaway and the general store to talk to the town engineer, but that doesn't uncover anything. Frank suggests Callie Shaw and Iola Morton join them and apply for waitress jobs at the restaurant. Joe and Chet go back to Bayport to talk to Callie and Iola. Frank and Biff stay in Rockaway and go back to the general store. Mr. Hardy calls while they are at the store and tells them he has found a connection between the restaurant and Cadmus Quill. The girls come to Rockaway and apply for jobs at Palais Paris, but aren't hired. When they get back to the car, they discover Biff has been hit on the head. As they drive back to Rockaway, their car is almost run off the road. When the group of friends meet up again, they decide to go together to the antique shop to pay for the spinning wheel and get Frank's watch back. While they are eating lunch, someone steals Chet's metal detector. The boys return to Palais Paris, find the metal detector, put it in the back of their car and start driving back to Bayport. Minutes later, there is an explosion in the car. When the police and ambulance come, Chet is taken to the hospital, and the Hardy boys are taken home. Frank and Joe's aunt, Gertrude Hardy, arrives shortly after the boys get home. The brothers go to visit Chet to see how he is recuperating and find he has had a visit from someone impersonating a reporter. While Frank and Joe are still there, Chet receives a threatening note. Mary Todd stays with the Hardy family. Frank notifies the police, and the Hardy boys decide to return to the Honeycomb Caves by boat. As they do, they see a light come from Commander Wilson's cave. The next morning, Frank and Joe go out with a local fisherman, and from the boat, they see suspicious activity and people on the shore. A storm forces them back inland, and the fisherman's wife meets the boat to help tow them to their dock. After the storm stops, the Hardy boys return to the caves and see evidence of a submarine. They discover more caves and tunnels in this cave that connects it to Palais Paris. When a raft from the submarine goes into the caves, the boys hitch a ride underwater and head to shore. Cadmus Quill interrupts the boys' investigation. As they escape, they use the shotgun in the cave to cause a blackout. Chet, Biff, the state police and Mr. Hardy arrive to help catch the spy and saboteur ring and rescue Frank and Joe. When everything settles down, the only person unaccounted for is Morgan Thomas Todd. Frank and Joe find out that Morgan Thomas Todd had been rescued from the submarine. He had been taken prisoner by the spy and saboteur ring while trying to investigate what he had learned while studying abroad. The criminals had been headquartered at Honeycomb Caves, and some of them had been building equipment to jam the radar on Telescope Hill. Morgan Thomas Todd and Mary Todd are reunited; Chet will get reimbursed for the metal detector; Frank and Joe will get reimbursed for repairs to their car; and the Bayport Times newspaper runs a story about the case. Mrs. Hardy hosts a celebration at their home. The boys receive an appreciation telegram from Kenworthy College. And Gertrude Hardy brings down the spinning wheel the boys had broken (and then bought) in the antique store. She has put the spinning wheel back together, and it turns out it really is an antique.