The Control Capsule is the glass "jar" in which Mother Brain resides in her appearances in Metroid, Metroid: Zero Mission and Super Metroid. Samus Aran destroys it with Missiles. It only requires one Missile in Metroid, which only creates an opening in the glass, but multiple Missiles in Zero Mission and Super Metroid. The Metroid-based microgame in WarioWare, Inc.: Mega MicroGame$! and WarioWare, Inc.: Mega PartyGame$! still requires only a Missile, but the opening made in the glass will be larger.
In the Metroid Manga, Mother Brain says that the Control Capsule is made by molecule transference of Zebetite, and it uses the same system that governs Zebes' Planetary Protection Shield. The Control Capsule is named in the Super Metroid comic.