Harry and Neville heave themselves onto thestrals, while Luna helps Ron, Hermione, and Ginny, who can't see the creatures, mount. Harry tells his thestral that he wants to go to the visitors' entrance of the Ministry of Magic, and the creatures take off. As they fly, Harry wonders how long Sirius can resist Voldemort. They fly until after dark, and then the thestrals dive into London. Everyone dismounts and Harry leads them to the telephone box. Ron dials the number and passes out badges with their names and "rescue mission" on them.
The fact that Luna remembered that people can ride thestrals means that Hagrid deserves some credit: his lesson on thestrals was detailed and interesting enough that his students are able to take what they learned and use it in order to accomplish their goals in the real world—which is exactly what a Hogwarts education is supposed to do.
The atrium at the Ministry is empty. Harry leads everyone past the Fountain of Magical Brethren and into the elevators. They descend to the ninth floor and follow Harry into the Department of Mysteries. The first room they enter is round and black, lit with blue candles and with identical doors all around, and as soon as the door shuts, the walls spin. Ginny mutters that it's to keep them from finding their way back out. Harry says that in his dreams, he goes through a room that glitters. He chooses a door and opens it. There's a tank containing brains inside. They return to the circular room, Hermione marks the door with a fiery X, and they choose another one when the circular room stops spinning.
The revelation that this circular room spins is a reminder that Harry’s dreams aren't actually reality. This shows that at this point, because he's lacking information, Harry has a very incomplete picture of what he's facing in the Department of Mysteries—and this means that he's not prepared for what he's going to find.
This room is a courtroom with an archway on a dais. It has a fluttering black curtain, and Harry hears people talking behind it. He whispers for Sirius. Luna says she can hear people talking on the other side of the arch too, but Hermione and Ron drag Harry away. As they leave the room, Hermione insists that the arch is dangerous. The third door they try from the circular room is locked, so Harry tries to use Sirius's knife to open it. The door stays locked and melts the knife. The next door is the room they’re looking for. Harry leads everyone between desks to a crystal bell jar. Inside is an egg that hatches, grows into a hummingbird, and then falls back into its egg. Then they enter a room with shelves, all filled with glass orbs.
The fact that both Harry and Luna—two people who can see thestrals—are the ones who can hear people on the other side of the veil suggests that it has something to do with the dead, and is tempting to those who have lost loved ones. This again shows that people who are grieving are more easily manipulated, given their heightened emotional state. The different rooms also give interesting images of what is studied in the Department of Mysteries: memory, death, and time.
Harry leads them to row 97, worried because he can't hear Sirius. They find the row and creep toward the end. Hermione quietly says that Sirius isn't here. Ron calls Harry to one of the spheres, which has Harry's name on the label. Harry reaches out to touch it, but both Hermione and Neville tell him not to. The orb is pleasantly warm, and nothing happens when Harry picks it up. Then he hears Lucius Malfoy's voice behind him, asking for the orb—the “prophecy.”
The appearance of Lucius Malfoy tells Harry that this is a trap—what Voldemort wants is the orb, and he never really brought Sirius here. This makes it clear that Voldemort was able to use Harry's love for Sirius and his lack of knowledge about his dreams to lure him here. Now, he's in grave danger without any adults to call on for help.