Harry, Ron, and Hermione stand in shock for a moment. When they hear Hagrid howl, Harry turns to head back for him, but Ron stops him and leads them all towards the castle. Darkness starts to fall around them and Scabbers continues to struggle. Harry notices Crookshanks stalking them. With a final twist, Scabbers breaks free and races away. Crookshanks chases Scabbers, and Ron throws off the cloak to chase Crookshanks. Harry and Hermione follow until they trip over Ron on the ground, Scabbers safely in his pocket.
Again, Scabbers's bid for freedom suggests that, at the very least, he's done leading his cushy life as a Weasley pet. This indicates that there is more to Scabbers than Ron or the Weasleys suspected, while also opening up the possibility that Crookshanks knows what's going on with Scabbers and chases him for this reason.
Before they can get back under the Invisibility Cloak, they hear something coming and a huge black dog leaps at Harry. It knocks Harry down, grabs Ron's arm, and starts dragging him away. Suddenly, something hits Harry, and he hears Hermione shriek too. He lights his wand and sees that they're under the Whomping Willow. The dog tries to drag Ron into the tree's roots, but Ron hooks a leg around a root. Ron’s leg cracks and he vanishes. Harry tries to run through the branches, but Crookshanks weaves through and puts his paw on a knot on the trunk. The tree stops moving. Harry tells Hermione that Crookshanks and the dog are friends, and all three of them climb into the tunnel after Ron.
When Crookshanks shows that he knows how to make the tree stop, it suggests that he knows more than Ron has previously given him credit for. While Harry and Hermione interpret his actions as allowing them to follow and save Ron, they later learn that he's actually leading them to Sirius Black—Ron is just an innocent victim in all of this. However, when they choose to go after Ron, it shows that they care more for his safety than their own in this case—they're acting like good friends intent on saving him.
When Harry and Hermione reach the end of the tunnel, they carefully raise their wands to see where they've ended up. They see a dusty room with smashed furniture. Hermione whispers that they're in the Shrieking Shack, and Harry notes that ghosts don't destroy furniture. They hear a creak upstairs and silently climb to a landing. They hear Crookshanks purring and a moan through a doorway and see Ron on the floor. Ron moans that it's a trap and "he" is an Animagus. The door shuts behind Harry and Hermione and they turn to see a sallow, stringy man behind them. It's Sirius Black.
Now that Harry is in the Shrieking Shack, he can start to put together the evidence before him that suggests that the shack isn't actually haunted—he'll need to reevaluate everything he knows about the shack with this new evidence. When they realize that the dog is Sirius Black, it does become puzzling why he didn't kill Harry, given that that's supposedly what he's after—there's more to the story.
Black disarms Harry and Hermione and, eyes locked on Harry, says that he knew Harry would come—Harry is just like James, and this will make everything easier. Filled with rage, Harry starts for Black but Ron and Hermione pull him back. Ron pulls himself to standing and tells Black that he'll have to kill them too if he wants to kill Harry. Black tells Ron to lie down so he doesn't hurt his leg more and says only one person will die tonight. Harry taunts Black about having gone soft in Azkaban and throws himself at Black.
When Black expresses care and concern for Ron while saying that only one person will die, it offers a few clues that he's not actually after Harry or either of his friends. Harry is so filled with rage by Black's words because at this point, he still believes that Black betrayed his parents. Because of this, Harry takes Black's comparison to Harry's father like he takes Snape's similar comparisons: as an offensive insult.
Black is too surprised to fight Harry in time. The two scrabble on the floor until Hermione steps in. Crookshanks tries to keep Harry from getting his wand, but in the end, Harry and Hermione get their wands and point them at Black. Harry reminds Black that he killed Lily and James. Black doesn't deny it but says Harry doesn't know the whole story. Before Harry can say anything else, Crookshanks settles himself on Black's chest. As Harry raises his wand, they hear footsteps downstairs. Hermione screams that they're upstairs with Sirius Black.
Crookshanks's behavior again suggests that Harry is understanding something incorrectly when it comes to this story. Notably, Crookshanks is also acting like a good friend here by protecting Black and therefore he leads Harry by example. When Hermione screams for whoever's downstairs, it shows that she still trusts all the teachers at school to care for her and take her concerns seriously.
Lupin bursts through the door, takes in the scene, and disarms Harry and Hermione. Then, he asks Black where "he" is. Black points at Ron and Lupin, confused, mutters that "he hasn't shown himself" and asks if they "switched" without telling him. Black nods, Lupin helps him up, and the two embrace. Hermione screams wildly that she's been covering for Lupin and Harry, furious, shouts that he trusted Lupin. Lupin asks to explain, but Hermione tells Harry to not trust Lupin, as he's been helping Black, wants Harry dead, and is a werewolf. Calmly, Lupin says that Hermione is only right on one count: he is a werewolf.
It's telling that everything Lupin says to Black makes little sense to Harry, Ron, and Hermione. This makes it abundantly clear that they don't have the whole story. When Lupin tells Hermione that she hasn't fully understood everything, it shows that Hermione's cleverness isn't infallible and, without proper information, even she can come to incorrect conclusions. Harry's sense of betrayal shows how much he trusted Lupin.
Ron whimpers and Lupin starts towards him, but Ron gasps for Lupin to get away from him. Hermione says that she figured it out after Snape assigned the werewolf essay. Lupin tells Hermione she's clever and says that the entire staff knows; her telling anyone wouldn't have done anything. Harry yells again that Lupin has been helping Black. Exasperated, Lupin throws Harry, Ron, and Hermione their wands and asks them to listen. He says that he was looking at the Marauder's Map, which he knows how to use because he helped write it, because he suspected that the trio would visit Hagrid.
Lupin's admission that the staff knows about him being a werewolf reminds the teenagers that they're not experts and, because they're still children to many, they're not privy to everything that goes on at the school. By giving the trio their wands back, Lupin shows them that he'll now treat them like adults and tell them the truth, as long as they act like adults and listen.
Lupin says that when Harry, Ron, and Hermione left Hagrid's, he saw that a fourth person was with them. He watched Sirius pull two people into the Whomping Willow. Ron insists that it was just him, and then Lupin asks to look at Scabbers. Hesitantly, Ron pulls Scabbers out of his robes. Black says that Scabbers isn't a rat; he's an Animagus named Peter Pettigrew.
This new information changes everything that the trio knows about Sirius Black and the reason he's in Azkaban. If Lupin is correct, this means that they'll need to entirely rethink what they believe is true and, most importantly, begin to treat the Ministry with caution.