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The story of Harry Potter Hogwarts Mystery takes place through a series of chapters.

First Year

Chapter 1 - Your Journey Begins

The player starts chapter 1 with a character customization screen. Here, you can make your avatar look like any number of combinations of preset variables. Once you're done with this, you'll be introduced to Rowan Khanna at Diagon Alley, who will serve as a sort of companion throughout the story. Once you've started your budding friendship, you'll be tasked with getting your wand from Ollivanders.

At Ollivanders, you'll learn about your brother, who was expelled from Hogwarts and went missing under mysterious circumstances. When you answer some questions, you'll receive a wand.

Chapter 2 - Welcome to Hogwarts

The player arrives at Hogwarts and attends the sorting ceremony at the Great Hall. The Sorting Hat will ask you what house you believe you should be in - what you choose here will be your house, along with your friend Rowan Khanna. After this, the player heads to their house's common room and talks with Rowan. Once this is done, you'll go to the Charms Classroom and Potions Classroom for lessons. The player will also encounter their bully, Merula Snyde, and they will have to choose how to deal with her.

Chapter 3 - Dealing with Trouble

This chapter starts with two new characters being introduced - the Prefect of the house that they were sorted into and Ben Copper. The player will be asked if they want Rowan Khanna to join them for the next stage, where Merula Snyde will trick them and the player will be attacked by Devil's Snare. Rubeus Hagrid saves them, and sends them to the Flying class. If the player has not already befriended Ben Copper, they will be given another chance here.

Rowan then asks the player if they want to play gobstones. Your choices here will dictate the game's end result. Merula then finds them and reveals that some research that suggests the player's brother ran away to join the Death Eaters. The player can respond with information revealing that Merula's parents were Death Eaters, or to let it be.

Chapter 4 - Revenge is Best Served Magical

The player starts this chapter by learning how to duel from their house prefect. They'll start by finding a duelling spell, which is located in the Dueling Book in the Artefact Room. Here, the player also learns about the Cursed Vaults, which is what their brother was looking for when he went missing. Rowan will then talk to the player about the Cursed Vaults, which grants an opportunity to build on the friendship.

Once this is done, you will begin preparing for the duel. First, talk to Professor Flitwick, who will teach you Expelliarmus. Then, the player goes to speak to Ben Copper in the Great Hall, where they can cheer him up. Rowan then says she found another spell, and from there, that they should speak to the Prefect to get ready for the duel.

Chapter 5 - The Duel

After talking to the house Prefect, you will test your newfound skills by duelling with Rowan Khanna. While duelling, you'll have three choices - Aggressive, Defensive, or Sneaky. Duelling functions somewhat like a rock/paper/scissors game, with Aggressive defeating Sneaky, Sneaky defeating Defensive, and Defensive defeating Aggressive.

Aggressive Defensive Sneaky
Aggressive Draw Loss Win
Defensive Win Draw Loss
Sneaky Loss Win Draw

When you win the duel, you and Rowan will find Merula Snyde bullying Ben Copper in the courtyard. When Merula attacks Ben with a spell, you have the choice of either attacking before Merula attacks you, or attacking after Merula attacks - essentially either attacking or defending. Once you make your choice, you will have to duel Merula. Once you beat her, professors Flitwick and Snape break up the scene, blaming the player for the duel.

Flitwick will then ask the player who began the duel. If you chose not to attack first, Flitwick will defend you. Either way, Snape will give you detention - if you attacked, for starting the duel, and if you defended, for learning unauthorized defensive magic.

Chapter 6 - A Curious Corridor

After the duel, the player meets Penny Haywood. Penny offers her friendship and help to the player. Afterwards, they find Snape, who tells them that, were he the headmaster, he'd have sent them away from school for their duelling - but Albus Dumbledore wants them to go through detention instead. Argus Filch interrupts, telling Snape about a vault in a corridor.

Merula follows them, thinking that they were talking about the Cursed Vaults. The player decides to follow Merula, and happens upon Snake talking to Filch, asking him who else knows about the vault and the ice. He then decides on telling Dumbledore about the vaults, suggesting it might be related to Jacob. The player wonders why Merula cares about the vaults. Afterwards, the player tells Rowan Khanna everything they saw. The player can convince Rowan during this conversation to join the player to find out more about both the Cursed Vaults and the ice around the grounds.

Chapter 7 - Class Matters

The player will talk to the House Prefect, who will ask them to spend a bit more time focusing on school work so that the House Points can be re-earned after having lost so many in the first six chapters. The player talks to Rowan Khanna, and they decided to help Ben Copper with his flying. They then find him in the Great Hall. Ben feels worried about flying, so the player offers to levitate him using Wingardium Leviosa to break his fear. Afterwards, Ben talks to Madam Hooch, and ten points are given to both the player's house and Ben's house.

During the class section of this chapter, the players will have to convince Flitwick to teach them the Flipendo after they are told they cannot learn it since they already learned the duelling magic in an earlier chapter. If the player is successful, they will learn the spell. In Potions class, Merula asks the player if they talked about what they heard in the strange corridor. The player can either tell the truth or lie. You can also later tell Merula to rotate your potion two more times and get ten extra points for your house, closing the chapter with 20 extra points for your house.

Chapter 8 - Preparing for the Room

Chapter 9 - Inside the Room

Chapter 10 - Year's End

Second Year

Chapter 1 - Year Two Begins

Chapter 2 - Growing and Shrinking