On the train, Harry meets Ron Weasley, a boy from a large but poor, pure-blood wizarding family, and Hermione Granger, a witch born to Muggle (non-magical) parents. Upon arriving at the school, the first-year students are sorted into four houses: Gryffindor, Hufflepuff, Ravenclaw, and Slytherin. As Slytherin is noted for being the house of darker wizards and witches, Harry begs the magical Sorting Hat not to put him in Slytherin. He is assigned to Gryffindor along with Ron and Hermione. Harry notices a professor, Severus Snape, giving him peculiar looks.
Harry begins learning wizardry and discovers more about his past and his parents. Harry inadvertently makes Gryffindor's Quidditch team (a sport in the wizarding world where people fly on broomsticks) as a Seeker while defending another student from Draco Malfoy, a Slytherin first year, learning that his father was also on the team.
One night, Harry, Ron and Hermione encounter a giant three-headed dog at the Forbidden Corridor on the Third Floor of the school. After the trio incapacitate an escaped mountain troll and Harry is nearly knocked from his broom by a curse during one of the Quidditch matches, the trio assume that someone is trying to get past the dog. Harry discovers the Mirror of Erised which shows a person's heart's desire. Headmaster Albus Dumbledore moves the mirror and advises Harry against looking for it. Using information let slip by Hagrid, Hermione discovers that the dog is guarding the Philosopher's Stone, an item that can grant its owner immortality. Harry concludes that his potions teacher, Severus Snape, is trying to obtain the stone. Harry gets caught out of bed at night wearing an Invisibility Cloak left for him by his father, and is sent to detention. While helping Hagrid in the Dark Forest, Harry sees a hooded figure drinking a unicorn's blood for its healing properties. The hooded figure then attempts to attack Harry, only to be scared off by an arriving centaur named Firenze, a close friend of Hagrid's. Harry concludes that the hooded figure was Voldemort and that Snape is trying to get the stone to restore Voldemort to full strength.
After hearing from Hagrid that the dog will fall asleep if played music and that he revealed this to a man in a local pub, Harry, Ron and Hermione conclude that Snape was the man in the pub and attempt to warn Dumbledore. Upon learning that he is away on business, the trio conclude that Snape will attempt to steal the stone that night and resolve to find the stone before Snape does.
They face a series of obstacles: surviving a deadly plant, flying past hundreds of flying keys and winning a violent, life-sized chess match. The trio use their skills to overcome the obstacles. Hermione uses her knowledge of spells to get past the plant, Harry uses his skills as a seeker to get past the keys and Ron uses his skill at chess to win the chess match. However, Ron is nearly killed in the chess match and Hermione stays with him as Harry goes on ahead.
In the final room, Harry finds out that it was not Snape who wanted the stone, but Defence Against the Dark Arts teacher Professor Quirrell. Quirrell reveals that he let the troll in and tried to kill Harry in the Quidditch match. He also reveals that Snape has been protecting Harry and trying to stop Quirrell all year. Then, Professor Quirrell forces Harry to look in the Mirror of Erised. Due to an enchantment placed by Dumbledore, Harry finds the stone in his pocket after looking in the mirror. After trying to get Harry to answer what he has seen in the mirror, Quirrell removes his turban and reveals Voldemort to be living on the back of his head. Harry tries to escape but Quirrell starts a fire by clicking his fingers to prevent his escape. Voldemort tries to convince Harry to give him the stone by pledging to bring his parents back from the dead, but Harry refuses. Quirrell then tries to kill him but Harry's touch prevents him from hurting him and causes him to turn into dust and die. When Harry gets up, Voldemort's spirit forms and passes through Harry, knocking him unconscious before fleeing.
Harry wakes up at the school's hospital wing. Professor Dumbledore explains that the stone has been destroyed and that Hermione and Ron are safe. Quirrell burned at Harry's touch because, when Harry's mother died to save him, her death gave Harry a love-based protection against Voldemort. Before Harry and the rest of the students leave for the summer, Harry realises that while every other student is going home, Hogwarts is truly his home.