She discovers that Dr. Bumby was an acquaintance of her father who had a predatory interest in her sister, Lizzie. The Truth and Revenge
Emboldened by her inner victory, Alice pushes Dr. Bumby into the path of an oncoming train, killing him. The Ending: Londerland
Alice previously believed the family cat, Dinah, started the fire by knocking over a lamp.
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.
Through her journey, she remembers that Dinah was in the room with her and could not have caused the fire.