The battle against March Hare and Dormy's Humongous Mecha. Alice and the newly-befriended Hatter find themselves face-to-face against the steampunk mecha, and the Hatter is swiftly removed, putting Alice at the mercy of the mecha. The mecha's arm rises, ready to splat Alice... then a giant teapot falls on its head. The mecha is swiftly destroyed, and amidst the desctruction, the Hatter drops down and lands with an unflinching kneeling pose.
The ending. To summarize, Alice confronts the person responsible for the fire and the Infernal Train, Doctor Angus Bumby, who started the fire to hide the fact that he had raped and murdered Alice's sister. Bumby appears to be pulling a Karma Houdini because nobody would believe a former mental patient over a respected psychiatrist. Alice appears to give up in despair, then turns around and pushes Bumby right into the path of an oncoming train. So satisfying.
Before that, the symbolism behind Alice breaking out of the doll body he forced her into and taking on her Wonderland form.
This also happens just before she pushes him onto the tracks. Alice appears to change from her grey-toned London form into her bright Wonderland form - and the look on Bumby's face implies he seesthis transformation happen.
What Alice says to Bumby when she confronts him:
Alice: You've used me, and abused me, but you will not destroy me!
The sheer awe-inspiring beauty of Cardsbridge. An endless expanse of sky filled with playing cards. The sheer beauty contrasts with the horrifying realization with you getting your first solid clues on what happened in the fire.
Interspersed with Alice's confrontation with Bumby are conversations Alice has with the Mad Hatter, the Caterpillar, and the Queen of Hearts, where they all call her out for being willfully ignorant to the harm Bumby was causing. The Queen (who has taken on the form of Lizzie, Alice's deceased older sister) gets special mention, as she essentially tells Alice to stop feeling sorry for herself, get off her ass, and actually deal with her issues.
Queen of Hearts: Make your survival mean something! Or we are all doomed!
Alice's◊Hysteria◊ form.◊ It's extremely satisfying when Alice is on the brink of death and suddenly becomes a temporarily invincible death-machine.