Act I

Luna Lovegood and Neville Longbottom wander the Department of Mysteries, chased by Death Eaters. The Death Eaters retrieve Tom Riddle's diary from a safe in the Ministry, but this is taken from them by Ron, who rescues Luna and Neville. The three join Hermione outside the Room of Death, but are again surrounded by foes ("This Is The End"). Harry appears and rescues the group. Mad-Eye Moody enters the scene, who Harry reveals to be Barty Crouch Jr. Crouch is apprehended by the Wizard Cops. Crouch leaves Harry with the ominous message that with the Death Eater's gone, his fame will fade.

Harry presents his girlfriend, Ginny, with Riddle's diary. Ron reveals his insecurities in his and Hermione's relationship due as she hasn't kissed him in several years. Harry realises he doesn't know what to do after leaving Hogwarts. Ron is given the keys to the family car, and he flies Harry, Hermione, and Ginny to Hogwarts to start the school year ("Senior Year"). They crash the car, killing Professor Sprout and the school's mandrakes, but Draco saves them from expulsion by headmaster McGonagall. Despite this, Harry refuses to acknowledge him as a friend.

In the Great Hall, Harry and Draco are announced as the two candidates for the coming Head Boy election. Gilderoy Lockhart is announced to be the new Defence Against the Dark Arts teacher and is quickly proven to be more popular then Harry ("Wizard Of The Year"). Believing it as a cause for his loss in popularity, Harry ends his relationship with Ginny, who turns to the diary for comfort. The diary shows her a flashback of Dumbledore first meeting Tom Riddle at an orphanage and Riddle's first day at Hogwarts; Ginny quickly falls under Riddle's spell ("Always Dance").

Hermione reveals her passion for fanfiction to Lockhart and he commissions her to write essays for each of Harry's school years. Draco and Harry begin their preparations for the coming Head Boy election, when Harry suddenly overhears the Basilisk. The group discovers Colin Creevey and an entranced Ginny in front of a message written in blood. The message declares that the Chamber of Secrets has been opened, and Harry sees the situation as an opportunity to regain his popularity among the students.

Ginny again writes in the diary and Riddle shows the aftermath of his first murder and his decision to visit his father's home ("When You Have To Go All The Way Home").

Back in the present, Harry takes Cho as his date to Nearly Headless Nick's Deathday Party, but he becomes jealous upon seeing Ginny with Seamus and Dean. Ron points out he took Ginny for granted. Lavender kisses Ron on the cheek, which he believes is a betrayal to Hermione. Harry ends up ruining the party and everyone leaves, angry with him.

After the party, Harry overhears the Basilisk a second time and discover Nearly Headless Nick petrified, they question Ginny who claims to know nothing before running away. The Golden Trio follow a trail of spiders to the Forbidden Forest, where they encounter Aragog ("Get In My Mouth"). Aragog tries to eat the three friends, but Hagrid appears to rescue them. Hagrid tries to cheer up Harry by reminding him of his heroism, but Harry is still worried about leaving school.

Ginny writes in the diary again and Riddle shows her of his time at his father's house. At first he enjoyed his grandparents, although they took advantage of his naivety, but his father turned out to hate him. Upon discovering they are muggles and they give him Snickers as a present, Riddle murders all of them.

Harry and Draco tie in the elections for Head Boy after everyone votes for Fozzie Bear instead. Lockhart proposes a wizard duel to settle the tie, and Draco intends to forfeit because he regards Harry as a friend. Harry insults Draco and goads him into fighting. ("Tonight This School Is Mine"). Draco uses his Serpensortia spell to conjure a snake, and Harry consequently reveals his Parseltongue ability before the entire school. This event makes Harry the principal suspect as Slytherin's heir. Draco is announced as the winner of the duel and as new Head Boy.

Harry laments his downfall while Ginny reads of Riddle's remorse ("When I Was..."). Harry decides to leave Hogwarts, and Riddle finally reveals himself to be Lord Voldemort before Ginny. Voldemort summons the Basilisk, promising it finer prey than vermin.

Act II

After Hannah Abbott is petrified, Professor McGonagall announces that the school will be closed unless the Chamber of Secrets is found and the Basilisk slain. The students blame Harry for this and Ron stands up for him convincing the others to find Harry, but Draco reveals Ron's 'cheating' on Hermione, upsetting her. In an attempt to make him jealous, she tries to flirt with Lockhart who instead tricks her into signing over the copyright for her Harry Potter essays.

Hermione runs into a possessed Ginny and watches Voldemort have Ginny her search for the Resurrection Stone, eventually grabbing the diary and seeing Voldemort, but is petrified by the Basilisk. In the infirmary, Ron cries over Hermione's petrified body and determines to find a way to save everyone, realising he doesn't care about being second-best ("I'm Just A Sidekick"). Ron discovers a note Hermione wrote; Draco and Ron drink Felix Felicis and Draco sets out to find the Chamber of Secrets, while Ron searches for Harry.

Ron runs into Lockhart, who gloats about how he has turned Harry's story into seven books and merchandise in order to extort money from muggles. He also revealed he purposefully drove Harry away and slandered him in the election, he attempts to obliviate Ron, but is chased by the Wizard Cops who had been working with Hagrid all year. Ron learns that Kingsley Shacklebolt intends to blow up Hogwarts to kill the monster, but Hagrid secretly frees Ron who steals the flying car.

Harry is horrified to find Godric's Hollow has destroyed his statue to replace with one of Andrew Garfield's Spiderman, but the construction worker gives him advice. The worker repeats what Dumbledore said earlier, revealing to have Dumbledore's beard underneath his own before vanishing mysteriously. Ron arrives and attempts to convince him to return, but Harry refuses and causes a distraught Ron to storm off.

Harry finds the Resurrection Stone inside his lucky Snitch, and the ghosts of his deceased family and friends appear to give him encouragement ("Everything Ends"). Ron returns after talking to the construction worker and they return to Hogwarts. The students stand up to the Ministry and with Ron, Harry, the Sorting Hat, and the Scarf of Sexual Preference, set out to slay the Basilisk ("Goin' Back To Hogwarts" reprise).

Inside the Chamber, Harry and the students are overpowered by the Basilisk. Harry succeeds in pulling the sword of Gryffindor from the Sorting Hat and slays the Basilisk, but is bitten in the process ("Harry Freakin' Potter" reprise). As Voldemort stands over a dying Harry, Harry stabs the diary with the sword, killing the fragment of Voldemort's soul and saving Ginny. Hagrid arrives with Fawkes, whose healing tears rescue Harry from near-death.

The petrified students recover from their frozen state following the Basilisk's death, except for Colin Creevey, who dies. Hermione joins the rest of the students in the Chamber. Ron pulls an engagement ring from the Scarf of Sexual Preference and proposes to Hermione, who accepts, having heard his song in the infirmary. Harry finally accepts Draco as his friend. Harry proposes to Ginny, who accepts, and the students rejoice ("Days of Summer" reprise). As Harry is taking in all the times he had at Hogwarts, Ron arrives to pick him up for the last time. Harry says goodbye to Hogwarts and leaves with Ron.

19 years later, Harry takes his son to platform 9¾ ("Goin' Back to Hogwarts" reprise), where he runs into Quirrell, but fails to recognize him. Voldemort and Quirrell are at King's Cross to see their daughter leave for Hogwarts. Voldemort has come to terms with his defeat, and says that Harry has taught him how to love and that it is okay to let go of things, even if it hurts.