Set a year after Alice’s release from Rutledge Asylum, the story follows Alice Liddell in 1875 as she lives in an orphanage in Victorian London under the care of Dr. Angus Bumby. Though she believes she is well, she still suffers from hallucinations of Wonderland.

During an errand, Alice is drawn back into Wonderland, where the peaceful land has been corrupted by the Infernal Train and the Ruin. The Cheshire Cat tells her the corruption was caused by an outside force, not by Alice, and she is urged to seek out former friends and foes for answers.

As Alice moves between Wonderland and reality, she learns more about the fire that destroyed her home and family. She discovers that Dr. Bumby was involved in her sister’s death and had been trying to erase her memories, while his Wonderland counterpart, the Dollmaker, is tied to the corruption of Wonderland.

Alice confronts both versions of Bumby, defeats the Dollmaker, and pushes Dr. Bumby into the path of an oncoming train. Afterward, she enters a hybrid vision of London and Wonderland, while the Cheshire Cat says she has found the truth that was worth the pain.