Inside the last room, Harry finds the Mirror of Erised and none other than Professor Quirrell. Harry registers his shock that the culprit wasn't Snape. Quirrell, no longer speaking with his stutter, launches in with an EvilLaugh and some EvilGloating. He explains that Snape only hates Harry [[SchoolyardBullyAllGrownUp due to having hated Harry's father when they went to Hogwarts together]]. Despite this, Snape has actually been trying to protect Harry all year and everything the Trio assumed Snape did was actually done by Quirrell. Quirrell, meanwhile, met and was corrupted by Voldemort the year he took off to travel the world.

Quirrell states the mirror is the key to finding the Stone and looks into it, but he only sees himself presenting the Stone to Voldemort. A mysterious voice says to "use the boy" and Quirrell brings Harry up to the mirror. Harry sees his reflection place the Stone in his pocket and then the Stone appears in his real pocket. Harry tries to lie about what he saw, but it doesn't work. The voice says he wants to speak to Harry face-to-face and Quirrell removes his turban, revealing the face of Lord Voldemort on the back of his head. Voldemort asks Harry to hand over the Stone, casually revealing he knows it's in Harry's pocket. He says that Harry doesn't have to meet the same end as his parents, claiming Lily wouldn't have had to die if she hadn't insisted on protecting him. Harry still refuses and Quirrell tries to seize him, but touching Harry causes Quirrell's hands to blister and burn. Harry falls unconscious in the middle of the ensuing struggle.

Harry awakens in the hospital wing three days later to witness his first Dumbledore Explains It All scene. Harry learns several things:
* Quirrell died, but Voldemort's spirit lives on. The Flamels have decided that destroying the Stone is for the best, feeling that they have lived long enough anyway. However, Dumbledore admits that [[SequelHook there are still other ways Voldemort could return to power]].
* Harry asks why Voldemort wanted to kill him in the first place. Dumbledore sighs very deeply and tells Harry that he is too young to hear the AwfulTruth, but promises that he will tell Harry [[Recap/HarryPotterAndTheOrderOfThePhoenixC37TheLostProphecy one day]].
* Lily's sacrifice left Harry protected by ThePowerOfLove, which is why Voldemort couldn't kill him as a baby and also why Quirrell couldn't touch him.
* It was Dumbledore who sent Harry the invisibility cloak.
* James and Snape did indeed hate each other, but there was an occasion when James actually saved Snape's life. Dumbledore speculates that Snape worked so hard to keep Harry safe because he wanted to be "even" with James.
* The Mirror gave Harry the Stone because he wanted to find it, but not use it.
* [[ArsonMurderAndJaywalking Dumbledore lost his liking for Bertie Botts Every Flavor Beans after eating a vomit-flavored one.]]

Some time later, Ron and Hermione visit Harry in the hospital and he tells them about his encounter with Quirrell. Ron suggests that Dumbledore knew what was happening all along and set up a BatmanGambit for Harry so that he could handle it. [[OnlySaneMan Hermione says that would be "terrible"]], but Harry disagrees, stating that "I think he sort of wanted to give me a chance... it's almost like he thought I had the right to face Voldemort if I could." Another day, Harry is visited by Hagrid, whom is upset that he accidentally helped Voldemort. Harry comforts him and he gives Harry a photo album with pictures of his parents.

Harry arrives at the end-of-year feast to find the Great Hall decked out in silver and green to celebrate Slytherin winning the house cup. At least that's what Dumbledore lets the Slytherins think before he starts dishing out some "last-minute points". He gives Ron fifty points for defeating the giant chess set, Hermione fifty points for solving the potion riddle, and Harry sixty points for "pure nerve and outstanding courage". This leaves Gryffindor and Slytherin tied. But Dumbledore continues with "There are all kinds of courage. It takes a great deal of bravery to stand up to our enemies, but just as much to stand up to our friends." And thus Neville Longbottom, who "had never won so much as a point for Gryffindor before", tips the scales to win Gryffindor the house cup.

The year ends and the students take the Hogwarts Express back to King's Cross. As Harry leaves with the Dursleys, he assures Ron and Hermione that he will have a good holiday:

"They don't know we're not allowed to use magic at home. I'm going to have a lot of fun with Dudley this summer...."