In "The Brainiac Trilogy" (penned by Roger Stern and George Perez) in Action Comics #647-649, Superman reviews recent events and realizes that Luthor and Brainiac must be working together. Brainiac, who seems to have some mental connection to Superman, knows that Superman is aware of him. He acts quickly, taking mental control over Luthor's aide, Happersen, and eventually the other LexCorp employees. He uses mechanical devices to strengthen his control.

In Action Comics #649, Brainiac tells Luthor that he worked for the Computer Tyrants on his home planet, Colu. When he failed them, his body was disintegrated. Somehow, his mind survived and was drawn across space to the brain of Milton Moses Fine.

Meanwhile, Brainiac's body is submerged in a biochemical bath while it is treated with recombinant DNA and bionic enhancements. Superman arrives just as Brainiac emerges from the tank, now green skinned, with a fit, trim and muscular body. His mustache and beard are yellow, and he has metallic devices attached to his skull and back.

Brainiac launches a mental attack on Superman, but once again is defeated by the power of Superman's mind. Brainiac manages to escape in a star-ship (later called his "head-ship"), designed as a robotic face. He promises to return, and Superman promises to be waiting for him.