The Rabbit takes out a dispatcher who is reporting to the Queen about the events at Wonderland Jail. The Rabbit enters the city and visits his old hideout, then reads his journal to remember everything. He receives a message from the Mad Hatter telling him to give his "regards" to the Queen. The Rabbit enters the nightclub where the Queen is supposed to be, and finds a secret underground laboratory, receiving a text from a mysterious person to find 3 tapes. After finding the tapes, the Rabbit watches them and learns about Dr. Burr and Project Oystercloud. Mary Ann leaves a gun for the Rabbit to use to kill the Queen. The Cheshire Cat activates the elevator, warning him not to go, but he goes anyway, and is about to kill the Queen until he sees Alice in the background. Suddenly feeling guilty, he is killed by The Queen. When The Queen leaves, Alice ambushes him and kills him.
- Go into the city and pick up a Shiny and/or a Brick.
- Use either one to get into the hideout.
- Read the journal (optional), and then listen to the messages on your answering machine.
- Call Mary Ann and the Hatter before leaving the hideout.
- Take out Tweedledee and Tweedledum with one of two methods: use a Metal Pipe to kill them, or buy a mushroom from Rulio, then poison their drink.
- Dispose of the metal pipe to go through the metal detectors.
- Raise the temperature up to 90 degrees, then check the bathroom mirror.
- Call the number left by the Hatter.
- Check the slot machine, and change the odds to 1 to 1.
- After winning, go in the bathroom and one of the toilets will be replaced with a secret door.
- Attempt to go up the elevator, then observe Dr. Burr's body.
- Find the 3 tapes (1st tape always changes, but not too far, 2nd tape is in the dumpster, and the 3rd can be retrieved from Rulio).
- Watch the three tapes.
- Get the gun from Mary Ann.
- Go up the elevator to face The Queen.
- Use the Shiny/Mushroom combo for the Brain Medal, or use the Brick/Pipe combo for the Brawn medal.
- One of the numbers in the bathroom is for Boris, who if called, will send a text message saying "Alive slice", which mixed around becomes "Alice lives".
- One of the numbers in the bathroom is for the March Hare, who complains about people who carry bells around but don't actually use them, referring to what the player does the entire series.
- The Barsinger is quite possibly Mary Ann.