Umbridge immediately addresses Hermione/Mafalda and drags her along to the Muggle-born Registration hearing she's going to. Harry gets out of the elevator, still disguised as Runcorn, and has a chat with the new Minister of Magic (who's under Voldemort's control), the unfortunately-named Pius Thicknesse.
Harry and the Minister part ways, and he begins his search for Umbridge's office. He gets distracted by some anti-Muggle propaganda pamphlets, which claim that Mudbloods (Muggle-born wizards) do damage to wizarding society. Soon enough, though, he finds Umbridge's office; he's enraged to see that she's stuck Mad-Eye Moody's magical, all-seeing eye on her door. So that's why they couldn't find Moody's body.
Umbridge has gotten herself pretty high up in the Ministry – she's senior undersecretary to the Minister and also, unsurprisingly, head of the Muggle-Born Registration Commission. We can recall her anti-Muggle sentiment from Book 5, Order of the Phoenix.
Harry distracts the wizards and witches in the area, and sneaks into Umbridge's office, which looks just like her old office at Hogwarts – it's covered with doilies and ornamental plates with pictures of sickeningly cute, prancing kittens.
He can't find the locket anywhere, but he does find some items of interest – a file on Mr. Weasley, saying that he's a probable connection to "Undesirable No. 1" (Harry himself), and that he's being tracked by the Ministry.
Harry's about to leave, but gets distracted by a copy of Rita Skeeter's book, The Life and Lies of Albus Dumbledore; inside, he sees a picture of a teenage Dumbledore and a wild-looking, unknown other boy, apparently a friend of his.
Before Harry can leave, Thicknesse shows up (Harry manages to hide himself beneath the Invisibility Cloak before the Minister notices him). Thicknesse writes a note to Umbridge, while Harry sneaks out.
In the elevator, Harry runs into disguised Ron. Before they can touch base, though, Mr. Weasley enters the elevator.
Mr. Weasley strikes up a conversation with Ron/Cattermole about Yaxley's raining office; Ron runs out at the next floor. He's replaced by another Weasley, the estranged Percy, who sees his father and immediately gets out at the next stop too.
Now it's just Harry/Runcorn and Mr. Weasley. Mr. Weasley coldly tells the man he thinks is Runcorn (who's apparently a really bad guy who has betrayed a wizard who tried to fake his family tree) that he'll have to face the consequences of his actions.
In turn, Harry tries to warn Mr. Weasley that he's being tracked, without dropping his cover. We're not sure if it works or not.
Harry heads down into the courtroom where the Muggle-born trials are being held. There are dementors everywhere, and Umbridge and a tribunal of other wizards are coldly sentencing people to imprisonment. The next prisoner is Mary Cattermole, the wife of Reg Cattermole, who Ron is impersonating. Hermione/Mafalda is also there, keeping records.
Harry, wearing the Invisibility Cloak, creeps up behind Hermione. They observe as Umbridge and Yaxley question poor Mrs. Cattermole.
Hermione notices Umbridge wearing the Horcrux locket – she asks about it, and the loathsome former professor claims that it's a family heirloom. Liar!
Harry can't take it anymore. He Stuns Umbridge and Yaxley, and throws off the Cloak; he sends his Patronus to get rid of the dementors, and saves all of the Muggle-born prisoners. Ron stumbles down, and the three friends smuggle all of the prisoners out of the Ministry, telling them to go into hiding.
Yaxley awakes and figures out what's going on. Hermione, Harry, and Ron manage to Disapparate before they get caught.