Nineteen years have passed since the events of Harry Potter and the Deathly Hollows. Harry is now a grown man and an overworked employee of the Ministry of Magic. He’s married to Ginny Weasley, and their children are James, Albus and Lily. As the story begins, the Potter family is taking the nervous Albus to catch the train for his first year at Hogwarts.
The school’s students are divided into four houses, and Albus fears he may be chosen for the Slytherin house. Represented by a snake, Slytherin is known as a house of Dark Magic. Albus doesn’t believe it is a fitting place for brave wizards. At the train station, the Potters run into Ron Weasley and Hermione Granger, who are now married and have two children. Hermione is the Minister of Magic. Their daughter, Rose Weasley-Granger, is also attending Hogwarts for the first time.
On the train ride, Rose lectures Albus about the importance of falling in with the right people at school. She’s distraught when Albus immediately befriends Scorpius Malfoy. Scorpius is the son of Harry’s Hogwarts rival, Draco. Rumor has it that Scorpius may be the biological son of Voldemort, the evil wizard who killed Harry’s parents and tried to kill Harry.
Some suggest Draco and his wife couldn’t have children, so they used a Time-Turner to send Scorpius’ mother back to Voldemort’s time. They supposedly did this to provide a powerful heir to the Malfoy line. At Hogwarts, the sorting hat chooses both Scorpius and Albus to be in the Slytherin house.
The next few years are only briefly depicted. Albus continues to dislike Hogwarts, where he repeatedly fails to live up to his famous father’s legacy. The relationship between Harry and Albus grows increasingly tense. When a man with an illegal Time-Turner is arrested, Harry and Hermione secretly ponder how to handle the situation. Hermione hides the time travel device in her office.
One evening, an elderly Amos Diggery comes to visit Harry at home. Nearly two decades earlier, Voldemort killed Diggory’s son, Cedric, simply because Cedric was with Harry. Amos plays on Harry’s guilt by mentioning he’s heard the ministry has seized a Time-Turner. He asks Harry to allow him to use it and get his son back. Harry denies the Time-Turner rumors. Albus overhears the conversation. As he eavesdrops, he meets Amos’ niece, Delphi, who is also listening.
As Albus starts packing to return to school, Harry gives him a small blanket. It is the last thing Harry has from his mother. Albus complains that it’s a useless gift. In anger, Harry and Albus tell each other they sometimes wish they weren’t related. Albus runs from the room as Harry pleads for him to come back. Harry begins having bad dreams, and his scar begins to ache again.
On the way back to school, Scorpius tells Albus about the Triwizard Tournament, which hasn’t taken place in two decades. Scorpius says during the last one, Harry and Cedric Diggory were transported to Voldemort. Voldemort called Cedric a spare, or a useless extra person in the situation, and killed him. Albus grows indignant, convinced his father lied to Amos about the Time-Turner. He decides he will help right one of the wrongs of the past by saving Cedric. Albus and Scorpius sneak off the train and make their way to St. Oswald’s Home for Old Witches and Wizards. They find Delphi and Amos and vow to get Cedric back.
Delphi makes a potion of Polyjuice for herself and the boys. After drinking it, she looks just like Hermione. Albus looks like Ron, and Scorpius is the spitting image of Harry. They enter Hermione’s office to search for the Time-Turner. They’re almost caught by the real Harry and Hermione, who are discussing what to do about Hogwarts’ message that Albus and Scorpius are missing. Albus (as Ron) keeps them from discovering their look-alikes. Then the kids rifle through Hermione’s magical bookshelf until they find the Time-Turner.
Based on a dream of Harry’s, the adults head toward the Forbidden Forest to search for the boys. There, Harry runs into a centaur with whom he fought in the Battle of Hogwarts. The centaur tells Harry there is a black cloud around Albus that could endanger everyone.
The boys use the Time-Turner to go into the past. There, they begin to watch the 1995 tournament. They have just managed to disarm Cedric when they are sent back to their normal time. They discover the Time-Turner only allows them to spend a few minutes in the past. They find themselves back in the present with their parents. Albus, who has broken his arm, collapses.
In the next scene, Albus sleeps in a hospital bed with Harry at his side. Professor Dumbledore’s image visits Harry, and Harry asks for advice about how to protect his son. Dumbledore urges him to discover what is wounding Albus. When Albus wakes, he lies to Harry about where he had gone. Harry tells Albus what he’s heard from the centaur. He vows to set measures in place to monitor Albus’ movements. He also says Albus may no longer associate with Scorpius.
As Albus becomes indignant, Ron enters. Albus discovers he and Scorpius have somehow changed the past. In this timeline, Ron isn’t married to Hermione, and Rose was never born. Albus also learns he is now part of the house of Gryffindor.
Harry makes good on his vow to keep Albus under surveillance. A sad Albus and a hurt Scorpius continue to pass each other at school. Delphi convinces Scorpius to talk to Albus and restore their friendship. Together, the boys make another trip to the tournament in 1995 to save Cedric. Scorpius returns to the present, but Albus isn’t with him. Scorpius learns that, because of their actions in their latest time travel, Harry died years ago. Albus does not exist, and Voldemort rules.
In part two, Scorpius tries to get his bearings in his current reality. He learns his father, Draco, has been involved in torturing and killing Mudbloods. He finds out Severus Snape is still alive in this reality, so Scorpius visits him. Snape takes Scorpius to Hermione and Ron, who are members of an underground rebellion. They piece together the reasons the most recent time travel went awry. Snape, Hermione and Ron travel back in time with Scorpius. Dementors appear, and Ron and Hermione distract the creatures so Snape and Scorpius can finish their mission.
The dementors suck out Ron’s and Hermione’s souls. A little later, dementors kill Snape as he helps Scorpius escape. As Scorpius emerges back into the present, Albus is with him once again. Scorpius says the Time-Turner is gone. The headmistress lectures the boys for breaking so many rules and chides Hermione for keeping the Time-Turner in the first place. Scorpius later tells Albus that he still has the Time-Turner. As the boys are deciding how to destroy the device, Delphi appears. They learn she is Voldemort’s daughter. She breaks their wands and steals the Time-Turner.
Harry and Draco visit Amos Diggery and learn Delphi was not his niece as she had said. Meanwhile, Delphi kills one of the boys’ classmates and takes Albus and Scorpius back in time with her. She informs them that she wants the rebirth of the Dark in the form of Voldemort’s return. She wants them to help her humiliate Cedric so that he will become evil and pave the way for Voldemort’s victory. They thwart Delphi’s plans, so she destroys the Time-Turner and traps the boys in 1995.
The adults, having discovered Delphi’s plan to resurrect Voldemort, try to determine what’s happened to the boys. Draco confesses to Harry that his father had a Time-Turner built. They talk about using it, but they realize it won’t do any good since they don’t know where or when to find their sons.
Albus and Scorpius decide they must get a message to their fathers in the future. They leave a magical note on the blanket Harry’s mother gave him, telling Harry where to meet them in the past. Harry discovers Albus’ message. He, Ginny, Ron, Draco and Hermione travel back to the time at which Voldemort killed Harry’s parents.
There, they meet the boys. They believe Delphi will try to meet her father there and change the course of history for the worse. To draw her out, Harry takes on the form of Voldemort. They battle, and he captures Delphi with the help of his friends. Harry must decide whether to change the course of history by stopping Voldemort from killing his parents.
Ultimately he decides to let history play out as it did originally so he and his friends and family can go home. It’s painful for him to watch. Back in the present, Harry and Albus begin to mend their relationship. Harry also starts to deal with some of his crippling memories involving Voldemort.