The book begins at Number Four, Privet Drive, where Harry lives with his aunt, uncle, and cousin Dudley. Harry is forlorn because he has not heard from his friends Ron Weasley, Hermione Granger, and Hagrid since returning to Privet Drive at the end of his first year at Hogwarts School of Witchcraft and Wizardry. Over breakfast, Harry’s uncle tells him that while his business guests visit that evening, Harry is to stay in his bedroom and not make a sound. Harry agrees and retreats to his bedroom, once Dudley’s second bedroom, only when he arrives, he is not alone. He finds Dobby the house-elf there. Dobby issues a warning that Harry must not go back to school this year. He tells him terrible things will happen there. Harry insists he must return to see his friends, if nothing else, and Dobby tries to convince Harry that his friends do not like him since they did not write him any letters. Harry learns that Dobby has taken Harry’s letters from his friends all summer, and tries to retrieve them. Dobby escapes the room and goes downstairs, where he uses magic to destroy Uncle Vernon’s business dinner, hoping that the use of magic at home will get Harry expelled.

Harry does not get expelled and returns to Hogwarts, but not before a harrowing trip to Diagon Alley to pick up his books and supplies for the year. When travelling by Floo network, he accidentally ends up in Knockturn Alley, where he sees Draco Malfoy and his father, Lucius, a known Death Eater and follower of Lord Voldemort. Harry suspects them of malicious plans for the school year. 

Harry and his friend Ron miss the train to Hogwarts—another of Dobby’s attempts to keep Harry safely out of school—and fly Ron’s dad’s flying car to Hogwarts. They crash land but manage to get to school safely despite Professor Snape wanting to expel them for damaging the Whomping Willow tree with the car.

The school year gets underway, with Ron’s younger sister, Ginny, sorted into Gryffindor with Harry, Hermione, and the other Weasley brothers. Harry and Ron quickly learn that their new Defense Against the Dark Arts teacher, Gilderoy Lockhart, does not know what he is doing. Lockhart embarrasses himself on more than one occasion, including when he tries to demonstrate how to duel with Professor Snape and is easily disarmed. Strange things start happening at Hogwarts. Caretaker Argus Filch’s cat is petrified. Students and a ghost are petrified too. With rumours that the heir of Slytherin has returned to Hogwarts to cleanse the school of anyone who is not a pureblood. When Harry’s capability to speak Parselmouth—the language of snakes— becomes known, many presume he is the guilty party. It does not help that he always seems to be nearby when students are attacked. Harry, Ron, and Hermione begin to investigate who might be the heir. Harry suspects Draco, so he and Ron use Polyjuice potion to disguise themselves as Draco’s friends' Crab and Goyle. They ask Draco about the heir, who is opening the Chamber of Secrets to release a deadly monster. Draco is not the heir, and they are almost discovered in their flight from the Slytherin common room. 

Harry finds an old journal that writes back to him. The journal offers to show Harry who opened the Chamber of Secrets fifty years ago. Harry finds that Hagrid was suspected and expelled. He and Ron visit Hagrid to ask him about it, but Hagrid is arrested, and Professor Dumbledore is forced to step down as headmaster. Hagrid leaves a clue for Ron and Harry that leads them into the Forbidden Forest, where they meet Aragog, Hagrid’s pet Acromantula—a giant spider—who was incorrectly accused of being the monster from the chamber. Aragog tells them a student died, but it was not his or Hagrid’s fault. Harry and Ron narrowly escape Aragog’s family of ravenous spiders with the help of Mr Weasley’s car, which has taken to roaming the forest on its own. Meanwhile, Hermione has been petrified, joining the other petrified students—and cat—in the hospital wing. Harry and Ron go to visit her and find she is clutching a page defining “basilisk” torn out of a book on which she’s written the word “pipes.” Harry realizes the monster is using the plumbing to move around the castle, and that the student who died must be Moaning Myrtle, a ghost that inhabits one of the girls’ bathrooms. Harry and Ron listen to Myrtle’s story about her death.

There is another attack. As Harry and Ron hide in a cabinet in the teachers’ lounge to eavesdrop on the teachers, they hear that Ron’s sister, Ginny, has been taken into the Chamber of Secrets. Harry and Ron try to enlist the help of Gilderoy Lockhart, who turns out to be a coward and a fraud. They drag him along, and he tries to obliterate their memories. However, the spell backfires; Lockhart loses his memory and part of the cave collapses, separating Harry from Ron and Lockhart. Harry goes on to the Chamber of Secrets, where he learns that Ginny mistakenly brought to life a part of Voldemort’s spirit through the journal. Voldemort, known also as Tom Riddle, sets the monster—a basilisk—on Harry. The basilisk has the power to kill anyone who meets its gaze. Fawkes, Dumbledore’s phoenix, comes to Harry’s aid and blinds the basilisk. Harry then destroys it with the sword of Godric Gryffindor, which appears to him. However, he is poisoned by the basilisk’s bite. Harry uses one of the basilisk’s fangs to destroy the journal—and Voldemort—thus saving Ginny.

Fawkes heals Harry with his tears and flies Harry, Ginny, Ron, and Professor Lockhart out of the chamber. Dumbledore and Hagrid return, the petrified students and cat are restored, and Hogwarts is once safer.