At the very end when the true face(s) of the Red Queen are revealed, the mouth opens and reveals the Hatter. Why the Hatter? Makes sense from a few things:
The Hatter's voice is also that of Alice's father in the opening cutscene. He represents Alice's deceased father in a way (while the Red Queen perhaps represents her mother indirectly)
Alice lived in an asylum for awhile - the Hatter would eaisly resemble a doctor - just like the Tweedles
The Mad Hatter could also be an orderly. Orderly. That's why he's so obsessed with order.
