After visiting Fred and George’s new shop, Weasley’s Wizard Wheezes, Harry, Ron and Hermoine accidentally saw Draco Malfoy and her moher Narcissa sneaking. They followed them as they go inside Borgin and Burkes, On the way to Hogwarts, Harry uses his Invisibility Cloak and some Peruvian Darkness Powder from Weasley’s Wizard Wheezes to spy on Malfoy, but ends up getting no new information. Draco realizes Harry is there and immobilizes him, breaks his nose, and leaves him hidden under his Invisibility Cloak. Shortly after, Luna Lovegood finds Harry using her Spectrespecs and gets him off the train in time.
Amids the ceremony PRofessor Dumbledor announced that Proffesor Snape is the new Defense against Dark art teacher while Proffesor Hurace Sughorn will takes Snape's place. On the first day of their class Proffessor McGonagall informs Harry that since Snape is teaching Defence Against the Dark Arts, he and Ron can take N.E.W.T. Potions with Professor Slughorn instead of dawdeling. The boys use spare textbooks for the class, and Harry sees his very old copy is filled with footnotes and revisions that allow him to excel in Potions. This eventually leads to him winning a vial of the luck potion, Felix Felicis. Hermione, still envious of Harry’s success, looks to see who the book belongs to, finding only the alias of " THE HALF BLOOD PRINCE". In a private meeting in his office, Dumbledore shows Harry his memory of when he first met a young Tom Riddle. They learn from this that Voldemort likes to collect “treasures” from others. Dumbledore reveals that Slughorn has information valuable to Voldemort’s downfall and asks Harry to get to know Slughorn better.
One day, the trio witnessed Katie Bell being cursed by a necklace she was carrying up to the school. McGonagall and Snape learn that Katie was under the influence of the Imperius Curse; She was originally told to bring the necklace to Dumbledor and Harry assured that Dreaco was behind it.
Ron is a bundle of nerves at breakfast before a Quidditch match against Slytherin, where he is set to play the role of Keeper. Harry passes him some pumpkin juice. Luna sees that Harry had slipped something into Ron’s cup and Hermione is incensed that Harry would use Felix Felicis when it is banned from organized sports. Gryffindor wins the game against Slytherin after Ron saves every goal, and he is a hero and the centre of attention at a party to celebrate their success. Harry explains to Hermione there that he only made it look like he slipped something into Ron’s drink. After Lavender Brown kisses Ron, Hermione runs from the room, crying and Harry goes after her. He finds her crying in a corridor and consoles her. Hermione tells Harry that she knows how he feels when he sees Ginny with Dean Thomas and admits to having feelings for Ron. Later in the Library, Hermione and Harry discuss Slughorn’s Christmas party. Hermione warns Harry to be wary of who he goes with: Romilda Vane has been trying to slip Harry a Love Potion all year because she believes that "he is the CHOOSES one". Harry goes to the party with Luna and Hermione goes with McLaggen, who proves to be an unwise choice. Snape comes to deliver a message to Harry from Dumbledore telling him that he is traveling and escorted Malfoy away from the party when he tries to crashed.
At Christmas, Harry joins the Weasleys at the Burrow. He, Lupin, Tonks, and Mr. Weasley discuss what Harry overheard during Snape and Malfoy’s conversation at the party. Remus adamantly insists that Dumbledore trusts Snape implicitly. Later in the night Harry and Ginny share a brief romantic moment where they almost kiss but is interrupted by the arrival of Bellatrix Lestrange and Fenrir Greyback who set a fire around the Burrow. As they intended, Harry, who still holds a vendetta against Bellatrix for killing Sirius Black, breaks through the fire and chases Bellatrix. Ginny manages to get past the fire and chases after him. Both Harry and Ginny are surrounded by the ambushing Death Eaters, but Tonks, Lupin, and Mr. Weasley arrive in time to block the attack in the field. Outnumbered, the Death Eaters leave; after Bellatrix sets fire to the Burrow.
Back at Hogwarts, Harry, in another private meeting with Dumbledore, is shown another memory in the Pensieve. It is a memory from Slughorn when a teenage Tom Riddle asks him about a rare magic. The memory turns out to have been tampered with by Slughorn, who is ashamed of the answer he really gave Riddle. Dumbledore tells Harry that he is the only one who can get the true memory from Slughorn, and he must. All of Harry’s attempts to get the memory fail. Frustrated, he heads back to his dormitory. Once there, he finds that Ron is in a swoon, obsessively saying that he’s in love with Romilda Vane. Apparently he ate some chocolates on Harry’s bed, which were meant for Harry, laced with a very strong love potion. Harry brings Ron to Professor Slughorn to cure him. After Ron is cured, Slughorn offers the boys a drink of mead. Immediately Ron falls unconscious, poisoned. Harry manages to save him by shoving a bezoar down his throat. Later, in the hospital wing, it is revealed that the poisonous drink was intended to be given to Dumbledore. Lavender rushes in to be with Ron, but becomes outraged to see Hermione there. She and Hermione get into a yelling row until Ron mumbles Hermione’s name in his sleep. Distraught, Lavender leaves. Everyone else decides to leave and let Hermione to tend to Ron.
In the Great Hall, Ron has been released from the hospital wing and Hermione is thrilled that Ron’s relationship with Lavender has ended, but is crestfallen that Ron doesn’t remember any of it. Harry talks to Katie Bell, who has recovered from being cursed, but doesn’t remember anything useful for him. He notices Malfoy leaving apprehensively, and follows him into a bathroom where he finds him crying. Harry accuses him of cursing Katie Bell. They duel; Harry casts the Sectumsempracurse he found in the Half-Blood Prince’s book. Harry sees the curse caused severe slashes on Malfoy’s body. Snape sees Draco lying in a pool of blood and heals him.
Later, in the Gryffindor Common Room, Ginny suggests that Harry get rid of the book. He and Ginny go into the Room of Requirement to hide it. Ginny tells Harry to close his eyes so he can’t see her hide the book and before he opens his eyes again, Ginny kisses him.
After Ron mentions Harry’s bad luck on getting the memory from Slughorn, Harry remembers that he still has the Felix Felicis Harry takes the potion and meets Slughorn on his way to Hagrid’s hut. Slughorn decides to escort Harry down to Hagrid’s and they find him about to bury a recently deceased Aragog. They hold an impromptu funeral. After a few hours and several drinks, Slughorn again reminisces about Harry’s mother. Harry goes on to tell Slughorn about his mother’s sacrifice, that he accepts his role as The Chosen One and to not let Lily Evans’ sacrifice be wasted. Slughorn gives in and hands Harry the memory.
The memory shows Professor Slughorn telling Tom Riddle about a dark piece of magic called a Horcrux. A Horcrux is an object used to keep safe a piece of one’s soul that has been split away from the body. If one’s body is destroyed, one does not truly die, as a piece of their soul is still alive. This explains why Voldemort survived the killing curse that rebounded upon him the night he killed Harry’s parents. Dumbledore tells Harry that he believes that Voldemort split his soul and created six Horcruxes with the seventh piece being in his body. Two have already been destroyed: one being a ring that belonged to Voldemort’s mother; the other being Tom Riddle’s diary. Dumbledore reveals to Harry that he thinks he has found another Horcrux and that he cannot retrieve it alone.
Dumbledore and Harry apparate to a seaside cave to find the third Horcrux. Within an inner cavern, Dumbledore takes Harry to the middle of the lake where he thinks the Horcrux is hidden. On the island there is a basin filled with potion. In order to get the Horcrux Dumbledore drinks it. The potion causes him to experience unbearable pain. On Dumbledore’s orders, Harry administers the rest of the potion to him and retrieves the Horcrux, which tuns out to be a locket. Dumbledore says he needs water. Harry attempts to fill the now empty bowl magically with water, but in such a dark place, no container will hold water conjured by magic. Dipping the cup in the lake Harry is pulled in by an Inferius. Dumbledore saves him by conjuring rings of blazing fire, protecting them and driving off the hoard of Inferi.
The two apparate back to the Astronomy Tower at Hogwarts. Dumbledore tells Harry to go find Professor Snape, but Dumbledore hears someone coming and makes Harry go below and hide. Draco ambushes Dumbledore in the tower. He tells Dumbledore that Death Eaters breached Hogwarts by using the Vanishing Cabinet in the Room of Requirement. He explains that he repaired it and that there is another in Borgin and Burkes. He goes on to say Voldemort has chosen him to kill Dumbledore, and that if he doesn’t, Voldemort will kill him. The Death Eaters arrive to the tower and goad Draco to kill Dumbledore. He manages to convince Draco that he doesn’t need to kill him and that he can keep him safe; Draco begins to lower his wand.
However, Snape appears and fulfills his vow to Narcissa by casting the Avada Kedavra on Dumbledore, killing him. The Death Eaters and Snape immediately escape Hogwarts; as they leave, Bellatrix destroys everything in the Great Hall and sets Hagrid’s hut on fire. Harry catches them up and attempts to duel Snape, but Snape easily overpowers Harry. Harry tried to use the spell "Sectumsempra" before Snape leaves and join the other fleeing death eaters, and he reveals to Harry that he is the Half-Blood Prince. Harry returns to the base of the Astronomy Tower and cries over Dumbledore’s body while Ginny consoles him, as the staff and students of Hogwarts raise their wands in respect to Dumbledore.
The next morning, Harry and Hermione discuss that the locket is a fake and there is a note inside it:
To the Dark Lord, I know I will be dead long before you read this, but I want you to know that it was I who discovered your secret. I have stolen the real Horcrux and intend to destroy it as soon as I can. I face death in the hope that when you meet your match, you will be mortal once more signed by R.A.B.
Harry then says that he will not be returning to Hogwarts, but instead he will be looking for and destroying the rest of the Horcruxes. Hermione says that he will not be going alone, as Ron and herself will help Harry on his quest rid the world of the Dark Lord once and for all. As they finish their talk they see Fawkes flying over the school, after one final turn the phoenix flies away from Hogwarts with Harry, Ron and Hermione watching him fly in to the Sunset.