Wishing to make his new home in the Earth-Two universe, the Commander had like his counterpart faced the Man of Steel in battle. While on Earth-One, Superman was joined by the Justice League and Teen Titans in averting an invasion, here it fell upon the native Justice Society with the visiting Justice League and the Champion family assisting them. In both instances, Brainiac and Commander found a worthy implacable enemy in the Last Son of Krypton, who led the fight to topple these intergalactic egomaniacs from their insatiable thirst for conquest. In Brainiac's case, it was through Superman's manipulations of the sun to cause power spikes in the robotic rogue's cerebral cortex which cause him to lose his memory and plotting capabilities. Seeking refuge in hyperspace, the villain to humanity would next appear in the void between universes, having created a floating replica of Metropolis complete with a horde of Supermen robots that lured the Legion and the original Kryptonian Crusader into a trap. A trap they managed to circumvent, causing Brainiac to once more escape only to return during the Crisis on Infinite Earths to lead a villain war against five Earths.
In the case of the Commander, it took the combined cognitive capabilities of the Champion children and their aunt coordinated by Doctor Fate to create a dimensional rift, one into which Superman and his JSA and JLA allies could thrust the tyrant. Seeking to return him to his own universe, the Commander forced himself to remain in Earth-Two's plane of existence, at the cost of his own essence dissolving into all of that universe's reality, while the League and Society (like the Legion and Superman above) were thrust through dimensions into the void between universes albeit briefly. Interestingly, just as around this time that Mekanique left Earth-Two for Earth-One alongside Commander Steel, before disappearing to a post-Crisis Earth.
However in the 30th century the original Brainiac form had reappeared and was in this future timeline consumed by a star going nova yet undergoing quite a different transformation from that of Stargrave, turning into storehouse of tremendous cosmic energy. In this form, the now insane android was intent of locating his most hated adversary in the form of Superboy, himself a member of the Legion of Super-Heroes, and of the offspring of his wayward progeny in the form of Legionnaire Querl Dox aka Brainiac Five. On one occasion, his genocidal tendencies seemingly led to the death of Ultra Boy, who was later located in inter dimensional limbo. Stargrave himself, although among the most powerful of villains in that era, was finally and decisively beaten by Dox never more to reappear.
Another android on Earth-Two had assumed the physical presence of Brainiac while possessing the awesome energies of Stargrave yet with the mental might originating from Doctor Anton Hastor. Hastor had hijacked on enclave of scientists determined to being an end to World War II by means of technology thought to be from the stars, and used it versus the All-Star Squadron. This evil entity was also defeated by its master's arch-foe the Hawkman alongside his fellow All-Stars, with the body scrapped in some government warehouse until this very day.