Chameleon Boy, who suspected this from the beginning, finally found proof when Brainiac's madness led him to an attempt to destroy the universe, utilizing the Miracle Machine, a device that turned thoughts into reality.
He was stopped by Matter-Eater Lad, who ate the machine, and both were committed to a mental institution, the energies of the Machine having driven Matter-Eater Lad insane as well.
It was claimed in Superboy #225 that Stargrave was actually the original Brainiac android, but the truth of this is uncertain.
When Stargrave murdered Ultra Boy's ex-girlfriend An Ryd, Brainiac 5, driven mad by Stargrave, framed Ultra Boy for the murder.
Brainiac 5's ingenuity led to the invention of, amongst other things, the Legion flight ring (perfecting an invention of the original Invisible Kid based on a metal discovered by Mon-El), the anti-lead serum that allowed Mon-El to leave the Phantom Zone and the force field belt which became the signature device of the character.