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Granger and Tonks are standing at the bottom of the stairs, just outside Harry's cell.

GRANGER: I may have to move quickly before a certain person becomes too settled in his opinions. Don't be alarmed; I will Disapparate as soon as I escape the range of the cells' Anti-Disapparation Jinx.

Granger flies up the staircase and Disapparates in midair, then reappears high above Hogwarts Castle. Then ze flies down to the wall of Dumbledore's office, causes the stone blocks to move aside by magic, and steps in. Dumbledore has new furniture, which is dark grey, and zir right hand is blackened. A piece of parchment and the Pensieve sit on Dumbledore's desk. Granger is nonchalantly putting the blocks back in place when Dumbledore speaks.

DUMBLEDORE: Ah, Hermione. But how...?

GRANGER: Please call me Granger; I am here on business. The castle defenses have a height limit and this office is not enchanted against intrusion through stone walls by air, but I'm not here to talk about clever magic. I'm here to discuss this.

Granger points at the parchment on Dumbledore's desk.

DUMBLEDORE: I was afraid you would say that.

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Approximate readability: 10.17 (705 characters, 149 words, 8 sentences, 4.73 characters per word, 18.62 words per sentence)

Dumbledore had to replace zir furniture after the fire. The Pensieve survived, though. (It's made of stone, and probably enchanted to be harder to break as well.)

Granger could have taken the Floo Network instead of using such a showy method of travel, but many people can access the Floo Network Authority records. Granger doesn't want any of zir enemies to be able to track zir location.

In the books, there are some sort of unspecified defenses that make it harder to fly towards Hogwarts by broomstick, in addition to the Anti-Apparition Charm and Anti-Disapparition Jinx that cover the castle. That might prevent Granger from using zir flight magic to enter the castle airspace. However, unless there's a hard barrier that blocks physical objects, there's nothing to stop Granger from falling to the interior of the shield and then flying the rest of the way as normal.