The battle against March Hare and Dormy'sHumongous 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 because he was raping 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.
Alice's◊ Hysteria◊ form.◊ It's extremely satisfying when Alice is on the brink of death and suddenly becomes a temporarily invincible death-machine.