Mother Brain usually resides in her central base on Zebeth, typically with a variety of minions at her command to do her bidding. Being a limbless brain in a jar makes it a bit difficult to accomplish physical things, otherwise. The minions also make for a convenient under-jar-slidey-goo. She generally dislikes being blasted by missiles, but hell... who wouldn't? Mother Brain has been the figurehead of all minions in the regular enemy-union, and thus they generally look up to and obey her.
Until she died that is. Yeah, Samus and Kraid went after her, found her clonatorium, found the central heart that keeps all of that running, and destroyed/devoured it. Kabutroid woke her up though. She was last seen preparing for her future battles with the Rinkas.