Magicant Theory

Magicant is actually a place that exists in all of our minds, but it can only be tapped into by something incredible, like the alien sculpture in the first Mother game or the ultimate fulfillment of the Sound Stone, which allowed Ness to enter this manifestation of our own memories and imaginations. It is somewhat a place also to represent our racial memory, an idea concocted by Jung that claims we all have common history passed down genetically by our ancestors. The impossibility of us being able to tap into the knowledge and magic of the place gives it the simple name "Magic-can't." Our heroes lose access to the place once they rid it of what didn't belong there, aka Queen Mary and Ness's Nightmare.

As for Queen Mary, she was sealed away into the mind of her son, or Ninten's grandfather in attempt to hide away from the evils of Giegue. She lived in a castle in the middle of the mind, thinking of the place as a reality, and she just continued into the minds of the "dynasty" or lineage of the family.