In the final confrontation, Alice faces the (Bumby’s Wonderland counterpart) on the Infernal Train while simultaneously confronting the real Dr. Bumby at the Moorgate train station.

Emboldened by her inner victory, Alice pushes Dr. Bumby into the path of an oncoming train, killing him. The Ending: Londerland

Alice destroys the Dollmaker, symbolizing her triumph over Bumby's psychological control.

Alice eventually realizes that Dr. Bumby molested and murdered Lizzie, then set the Liddell home on fire to cover his tracks. His hypnotic "treatments" were actually attempts to erase Alice's memories of his crimes so he could exploit her and other orphans for profit.