The movie reverses the order of the first scenes; the book starts with the scene at Malfoy Manor and proceeds with the Dursleys' departure. In the movie, Hermione is seen wiping the memories of her parents, something she only mentions in the book later on.
At home, Harry reads Dumbledore's obituary in the paper, written by his friend Elphias Doge. It mentions Dumbledore's uneasy relation with his brother Aberforth, the deaths of their mother Kendra and sister Ariana, and Dumbledore's rise to fame, mainly through his legendary duel with the dark wizard Grindelwald. The paper also announces an upcoming book by Rita Skeeter, in which she details a lot of slander and gossip about Dumbledore and his family, which angers Harry.
During the Dursleys' departure, there is an unexpected reconciliation between Harry and Dudley, where Dudley thanks Harry for saving him from the Dementors two years earlier (part of this scene was filmed, but deleted from the movie).
In the movie, Mundungus Fletcher is finally introduced in the scene where Harry is escorted out by the Order; Fletcher was already introduced in the novel "The Order of the Phoenix". Ron's older brother Bill Weasley was also introduced here due to his previous omissions from the films; in the books, he was properly introduced in "The Goblet of Fire" novel. In the book, the real Harry is escorted to the house of Ted Tonks, father of Nymphadora Tonks, and from there Apparates to the Weasleys' Burrow. Ted Tonks does not appear in the movie.
Harry, Ron and Hermione spend several days at the Burrow, doing chores and planning the mission together, of which they can't say anything to the others. Harry at first objects to Ron and Hermione's participation, but they are determined to help him anyway. Ron has even managed to disguise a ghoul as himself, which will mask his absence. Harry insists they should check for clues in Godric's Hollow first, but it is not safe there. Hermione has managed to find a book about Horcruxes, learning that they can be destroyed by Basilisk venom. As Dumbledore is dead, Grimmauld Place, the Order's old hideout, is no longer secret and can't be used anymore. Fleur Delacour's parents arrive for the wedding. Meanwhile, the Death Eaters are infiltrating the Ministry of Magic, and another breakout occurs in Azkaban.
Upon Harry's seventeenth birthday, he has a vision of Voldemort searching for a man named Gregorovich; the name is familiar but he dismisses the thought for the moment. His birthday is celebrated in the Burrow, and Harry can now perform magic outside the school without being detected. Scrimgeour arrives with Dumbledore's will as in the movie, but in the book, he and Harry get into another argument over Scrimgeour's unwillingness to give Harry the Gryffindor Sword. Later that night, Harry discovers the message on the Snitch (which occurs much later in the movie).
During the wedding, Harry is disguised with Polyjuice Potion as a Weasley relative. Victor Krum also attends the wedding, and he gets into an argument with Xenophilus Lovegood over the Deadly Hallows symbol the latter is wearing; Krum believes it was once the sign of the evil wizard Grindelwald, and takes Lovegood for a sympathizer. Harry suddenly remembers that 'Gregorovitch' is another famous wandmaker, now sought by Voldemort since Ollivander cannot help him any further. During his talk with Elphias Doge and Aunt Muriel, the latter confirms a lot of murky details from Dumbledore's past as described in Rita Skeeter's book, such as that his sister Ariana was a Squib (person from a magical family, but without magical powers herself); the family kept Ariana locked up out of shame, and she supposedly killed her mother during an escape attempt. Muriel even goes as far as implying that Albus killed Ariana out of revenge.
While staying at Grimmauld Place, the trio receive a Patronus from Ron's father, announcing the family is safe. Harry has another vision of Voldemort forcing Draco Malfoy to torture another Death Eater for failing to apprehend Harry. Harry finds an old letter from his mother to Sirius, thanking him for the broomstick Sirius bought for Harry's first birthday. The letter also mentions Bathilda Bagshot, prompting Harry to go there as Bagshot obviously knows a lot more. Hermione again refuses. Upon discovering who RAB is, they suddenly remember that they once encountered a locket they could not open during cleaning (occurred only in the novel "The Order of the Phoenix"); they suspect Kreacher of having retrieved it. Kreacher explains that Voldemort took him to the cave and used the Elf to hide it in the poisoned basin. Kreacher told Regulus, who, disillusioned by the Death Eaters, retrieved it himself and gave it to Kreacher to destroy, while dying himself in the cave. Since Kreacher couldn't destroy it, he hid it in the house, until Mundungus stole it. Grateful for the information, Harry gives Kreacher the fake locket.
While waiting for Kreacher to return with Mundungus and the locket, the three get a visit from Remus Lupin; he tells them about the Muggle-born registration commission, that the Ministry is looking for Harry under the pretense that he is a suspect in Dumbledore's murder, and that Lupin himself is to become a father as Nymphadora is pregnant. Lupin offers his help in the trio's search, but they get into a heated argument when Harry reproaches Lupin for wanting to leave his pregnant wife. Lupin furiously leaves the house.
The movie contains a scene of several Death Eaters searching the Hogwarts Express for Harry, which is not in the book.
Upon hearing that Severus Snape has become Headmaster of Hogwarts, Hermione picks up Phineas Nigellus' portrait and stuffs it in her bag, afraid that Snape might use Nigellus' portrait at Hogwarts to have him spy on Grimmauld Place. Harry has another vision of Voldemort murdering a family after demanding to know Gregorovitch's whereabouts. Hermione insists that Harry use Occlumency to block out those visions, but Harry finds them helpful.
The break-in into the Ministry is largely the same as in the movie, except for some small alterations. In the book, Harry searches Umbridge's office under his Invisibility Cloak, where he finds out that Arthur Weasley has the Trace on him; by coincidence, he and Ron later get into an elevator with Ron's dad. Harry tries to warn Arthur that he is Traced, but Arthur, unaware it is Harry in disguise, mistakes this as a threat, and leaves. The trio save more Muggle-borns present at the Ministry, advising them to leave the country. When they go into the fireplace and end up in the lavatory, Harry hears Yaxley coming after them, so he grabs Ron and Hermione and Apparates to Grimmauld Place. However, Hermione immediately Apparates them away to the forest where the Quidditch World Cup was once held, as Yaxley was pulled with them to Grimmauld Place, and now knows it is their hiding place (in the movie she Apparates immediately to the Forrest of Dean, where she had once stayed with her parents).
While in the forest, Ron insist that no one use the name 'Voldemort' any longer, as he feels the name is somehow jinxed (this later confirmed to be true upon Ron's return; speaking the name out loud allows the Death Eaters to quickly trace the speaker). They try to enter a small countryside village, but can't, due to the presence of Dementors; they venture to Tom Riddle's old orphanage, looking for a possible Horcrux, but the orphanage is completely replaced by offices. During one night in the forest, they eavesdrop on a conversation between a group of people, including Ted Tonks, Dean Thomas and two Goblins, who all fled from their homes. It appears that students at Hogwarts are subjected to severe punishments; a group, including Ginny, tried to steal the Gryffindor Sword from Snape's office, but were caught, and the Sword was sent to Bellatrix Lestrange's vault at Gringotts Bank. However, one goblin who saw the sword insists it was a fake. At any rate, no one seems to believe that Harry was responsible for Dumbledore's death.
Hermione questions Nigellus' portrait in her bag; he mentions that Dumbledore once used the real Gryffindor Sword to destroy a black ring; the sword is reinforced with Basilisk venom since Harry killed the Basilisk with it in the Chamber of Secrets, and can therefore destroy Horcruxes (in the movie they have no clue yet, trying to destroy the locket with conventional curses, until Hermione suddenly remembers that Basilisk fangs will do the trick, and they suddenly understand why Dumbledore left Harry the Gryffindor sword). Harry has some more talks with Nigellus' portrait later on, learning that the Hogwarts students are silently resisting Snape's rule.
There are scenes in the movie where Hermione ties her scarf to a tree for Ron, and Harry comforts Hermione by inviting her to a little dance, which are not in the book. Another scene exclusive to the film is where a group of Snatchers come dangerously close to the hidden camp, but then leave off.
When Harry and Hermione run out of ideas, they finally decide to go to Godric's Hollow; their only lead now is Bathilda Bagshot, who may known the location of Gryffindor's sword. In the book they disguise themselves as a middle-aged couple. The village has a war memorial, but this is a disguise for Muggles: wizards perceive it as a memorial of infant Harry and his parents. In the graveyard, they also find the graves of Dumbledore's mother and sister. Harry's old house bears an inscription, that it stands as a monument, invisible to Muggles. While invited inside by Bathilda, Harry's scar hurts, and he realizes that he is walking into Voldemort's trap. Nagini summons Voldemort, who suddenly Apparates inside, but Hermione is just able to Apparate them out. Half-conscious, Harry witnesses a flashback of Voldemort's memories from the night he killed Harry's parents.
Dumbledore's biography presents even more unsubstantiated rumors about Dumbledore and his family than Harry already read in the paper and heard from Aunt Muriel. However, one document written by Dumbledore himself clearly proves that Albus was once friends with Grindelwald, before he became a feared dark wizard, and that they had a shared view of wizards ruling over the Muggles for the greater good. This deeply conflicts Harry, as the Dumbledore he knew always strongly promoted equal rights for Muggle-born wizards. More anecdotal evidence points to Albus hiding his Squib sister out of shame, and her death as the point where his friendship with Grindelwald ended; apparently, Albus' brother Aberforth blamed Albus for the death, and punched him in the nose during the burial. Harry's trust in Dumbledore is starting to crumble.
At Xenophilius Lovegood's house, Harry notices a statue of Rowena Ravenclaw and her famous diadem, providing a clue for his later search. Upon hearing the story of the Deathly Hallows, they realize that Harry's Invisibility Cloak could be one of the Hallows, as, unlike other cloaks, its magic has never worn out over the years. When the Death Eaters arrive, Hermione causes an explosion and wipes Xenophilius' memory, while secretly Apparating themselves away to a field.
A large chapter spanning several weeks was excluded from the movie, where the Hallows and their alleged existence are further discussed. Harry now remembers that Voldemort's Horcrux ring had the symbol of the three Hallows engraved in it (he previously thought it was a family weapon), and realizes that the black stone set in the ring could very well be the Resurrection Stone, that had been passed to Voldemort's relatives, without he or any of them realizing. He also surmises that this stone is inside the Snitch. One night, they listen to a radio broadcast, which confirms the death of several people, including Ted Tonks. At the end, Harry inadvertently speaks Voldemort's name, which instantly removes the camp's magical protection and summons a group of Snatchers, who already have Dean Thomas and Griphook the goblin in their custody. In the movie, the three Apparate from Lovegood's house back to their old camp site, where the Snatchers, who found Hermione's scarf, are waiting for them. Dean is not with them and Griphook is already a captive at the Malfoy's.
The book does not specify how Hermione is tortured by Bellatrix (supposedly with the Cruciatus curse); in the movie, Bellatrix does it by carving the words 'mudblood' into Hermione's skin. When Wormtail comes to check on the prisoners in the book, he gets into a brawl with Ron and Harry; while choking Harry with his artificial hand, Harry reminds him that he once saved Wormtail's life. Wormtail spares Harry and is subsequently choked by his own hand. Harry has another vision of Voldemort killing an uncooperative Grindelwald in his cell, whereas in the movie, Grindelwald reveals to him who took the Elder Wand, and Voldemort simply leaves.
When arriving at Shell Cottage, Harry sees Voldemort, furious about Harry's escape, punishing the Death Eaters at Malfoy Manor. Finally, he is successful in closing his mind to the vision.
The closing scene of the movie (Voldemort taking the Elder Wand from Dumbledore's tomb) is another vision that Harry witnesses, although in the book it occurs after Harry has had a talk with Griphook and Ollivander (which happens in the next film).