The story's prologue is set in Highgate Cemetery, where Professor Alexis Fairburn, an Eton beak (Professor), is kidnapped by Wolfgang and Ludwig Smith. When he was kidnapped, Fairburn was tracing a tombstone, but leaves the piece of paper with which he was tracing. The story itself starts with young James Bond and his friend, Perry Mandeville (leader of the Danger Society) reminiscing the previous days events.
Out of the blue, a letter to Pritpal from Alexis Fairburn comes, regarding Fairburn's resignation from Eton. To House Master Codrose and Headmaster Elliot, the ‘mistakes’ were just made by Fairburn because of his scatterbrained personality and eccentricity, but Pritpal soon figures out that the mistakes were there for a reason. James and Pritpal work towards trying to decipher them - the first of them are easy - some wrong names in the letter (Luc Olivier and Speccy Stevens) translate into “Solve seven cryptic clues.”
However, they have to get several photographs of the letter, which has been confiscated by Cecil Codrose, before they can continue. Eventually, they get it and continue. They determine that they have to solve the puzzle of a certain crossword in the next The Times and eventually determine that “Gordian Knot” means that they must meet a man nicknamed “Gordius,” who is coming to Pritpal's next Crossword Society meeting. James decides to come along to the meeting, but all the man does is play a game of Hearts, during which time James wins five pounds. The man gives his name as “Professor Ivar Peterson,” who is a professor at Cambridge University. However, James and Pritpal do not believe him. James arranges with his friend, Perry Mandeville to go to Cambridge University, which will work as he is intending to go off to London on his father's birthday leave.
Before James can go to London, there is a break in at the school and the matron is forced to leave the school out of shock. James is sure that the intruder was intending to take something related to Fairburn. James decides to leave for London with Perry at once and learns that one more clue, when solved, says that Fairburn has actually been kidnapped and James realises that the former Maths beak is in danger. He and Perry drive to London in his Bramford and Martin. On the way, they spy an old Bentley that is for sale. Eventually, they arrive in London and James goes off to Cambridge University to find Professor Peterson. Eventually, he asks his porter if he can see him and he agrees. However, when he goes into his office, he discovers that Professor Peterson has been murdered with an Apache revolver bayonet. The killer is, in fact, still in the room and James flees before he can be attacked.
James then reads a letter that he took from Peterson's desk and finds the name “John Charnage” in it. Before he can work out what it means, the killer James had seen arrives in a Daimler vehicle with his accomplice. It is clear to the reader that the killers were Ludwig and Wolfgang, the two men who had kidnapped Fairburn. James flees in the Bramford and Martin, but the men give chase and eventually, James ends up in a river. He manages to escape the vehicle before it explodes and hides under a bridge.
James passes out from the cold and wakes up in a hospital. After managing to steal a suit and his shoes, James hitches a ride to Perry's house in a taxi. After a light breakfast with Perry, the two realise that “John Charnage” is actually Sir John Charnage, a local businessman whose father used to own a chemical factory. The two pay him a visit, but James is recognised as the boy that was seen leaving the scene of Professor Peterson's murder. He locks them in a room and leaves seemingly to call the police. James and Perry try and escape, but they are spotted and only narrowly escape by throwing a basket of groceries that a boy was delivering at Charnage. They flag down a taxi and manage to get to Hackney, where the Eton Mission is and for which Pritpal and Tommy Chong are working.
The group solve the remains of the puzzle and determine two things - they need to check Room 5 of The Royal College of Surgeons and then go to Highgate Cemetery. They go to the museum first and discover the name “Charles Babbage,” who had tried to invent two machines for solving mathematical problems that were basically and early computer and determine that Charnage is trying to build one of these machines. They then head down to Highgate cemetery and meet a tramp named Theo who is living in the cemetery. He casually tells them that the cemetery houses Karl Marx, the man who had come up with the idea of Communism and “the man who turned the Russian bear red.” At that moment, Wolfgang and Ludwig arrive at the graveyard and kill the tramp. James and Perry flee and split up. James hides in the trunk of the killers' Daimler and is led straight to Fairburn's kidnapper - Charnage. When they arrive, James sets alight the Daimler and, in the confusion, enters the building.
James finds himself in an old, abandoned Chemical factory and finds his way to a room marked “Hazardous Chemicals.” He steals a bottle of Potassium from it. However, he is discovered and is forced to escape. He discovers that the factory has been changed into an illegal underground casino. James tries to find a way out, but an American man who has just lost a fortune in the casino forces him to help him win back his money in Roulette, preventing him from escaping. Eventually, James is caught and taken to Charnage, who decides that he needs to kill him. To do this, he forces him to drink a large amount of Gin. Drunk and with a damaged liver, James is then dragged by Ludwig and Wolfgang to a barge and they prepare to throw him into the River Thames. In his drunken state, he works out the rest of the crossword and determines that the word “Bond” (in his name) must have the word “runner” and the letter “m” inserted into it, but cannot make sense of the results. He manages to escape, however, by throwing the jar of potassium he had taken from Charnage's factory at them, blowing Wolfgang's hand off and then throwing himself overboard.
After eventually making it to land, he wanders through East London in his drunken state and passes out in an alley. He wakes up to find himself surrounded by a gang of girls, who prepare to beat him up. However, by coincidence, he is in the town of Red Kelly (the boy he met during the events of SilverFin). The leader of the gang is Red's younger sister, Kelly, who immediately takes a shine to James. After getting some food at the local pub, he goes to Red's home and learns that Charnage's business had died several years before because the labourers were always dying. James rests for a few hours and eventually determines that Charnage must have been doing a deal with the Russians to build the computer that he is trying to build, the N.E.M.E.S.I.S. machine. Red inadvertently solves the last piece of the puzzle - one of the results James had got earlier, Brunnermond, was actually where a large explosion took place, near the Royal Docks. James realises that the machine is at the Royal docks, in a boat called the Amoras. They get to the Royal docks in an old mail train that Red has been using.
Upon arrival, James and Red's sister sneak up to the boat in a small rowing boat and hide in a bathroom. James locates Fairburn and the three escape to a nearby passenger ship, where they decide to shelter for the night. Kelly, who has demonstrated an interest in James since learning his identity, insists on dancing with him in the ballroom to some music played on an old gramophone. However, during the night, some intruders get onto the boat and search for them. They are attacked by Charnage's butler Deighton and a Russian man, but are rescued by Kelly's gang. They return to the Amoras and destroy the Nemesis machine, killing Wolfgang and Ludwig in the process and decide to go off and find the Russian in charge - Colonel Irina Sedova (Babushka). They track her down to an abandoned train tunnel and search. Before leaving for the search, Red's sister gives James a kiss. They eventually find Babushka, but she prepares to kill James. James manages to kill her henchman, and discovers a gun in his own pocket. He has it aimed at Babushka's head, but she pleads with him to let her go. James agrees and eventually his friends arrive to help him. He tells Perry Mandeville that he intends to buy the Bentley they saw earlier with the money he won at the casino.
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