Brain Powerd moves like a dream you can't quite remember, all mood and dread and Yoko Kanno's score doing the real talking while the plot dissolves into something intentionally unknowable. Tomino built this to feel wrong, to make you sit in a flooded world where you're never sure who Orphan actually is or why the Grand Cheres feel almost alive. It's not trying to explain itself. The atmosphere is the point, and it works because you stop needing answers and just accept the weight of everything falling apart.
In the near future, much of the Earth lies under the sea or has been wrecked by earthquakes. At the center of this upheaval is the mysterious Orphan, which may or may not have caused the disasters. Orphan wants to raise a ship hidden far beneath the ocean, an act that would wipe out every human except the few loyal to it. Its agents pilot mecha called Grand Cheres and hunt for enormous disks that sometimes appear, racing through the sky and devastating the land or cities where they crash. When a dying disk nearly kills Hime, a Brain Powerd emerges from it, a living mecha related to the Grand Cheres but distinct from them. Hime becomes its pilot, bound to it in a symbiotic relationship, and joins an international organization working to stop Orphan, or at least to save humanity if Orphan wins.