Kevin Smith's script
Although attempts to have Brainiac in a Superman film date back to Superman III, these were nixed for various reasons. When Kevin Smith was brought to write a reboot Superman film, which at the time was being written by writer Greg Poirier as Superman Reborn featuring Brainiac in a major role, Smith came up with his own ideas to use Brainiac in his story, as producer Jon Peters felt that Poirier's story didn't respect the Superman mythos.
In Kevin Smith's script, Brainiac is assisted by his robot L-Ron and sends Doomsday to kill Superman, blocking out the sun to render Superman powerless. As a result, Superman and Doomsday fight to death and both end up perishing after the battle. With Superman gone, Brainiac teams up with Lex Luthor, but the Eradicator, a Kryptonian robot whose technology Brainiac desires, resurrects Superman albeit still powerless, leading the Eradicator to give Superman an armor to defeat Brainiac until his powers are restored.
Among some other ideas producer Jon Peters asked Smith to include on his Superman Lives script were having Brainiac fight against polar bears at the Fortress of Solitude and making Brainiac give Lex Luthor an space dog as a gift, though the latter was just for merchandising purposes in the wake of the re-release of the Star Wars original trilogy.
Wesley Strick's script
When Tim Burton was brought to the project to direct the film after Robert Rodriguez turned down the offer, Burton had Smith replaced with Wesley Strick, as he hated Smith's script. However, upon reading The Death of Superman storyline, Strick understood many aspects of Smith's script and chose to retain some of them, including Brainiac's role in the story.
In Wesley Strick's script, while Brainiac's role in the story was mostly the same like in Smith's script, there was a major difference upon arriving on Earth. Once Brainiac arrives, he merges with Lex Luthor in a singly entity dubbed as "Luthiac". Beyond this, it's unknown how Luthiac's role developed from then on, but it's likely that Superman defeats it anyway.
Dan Gilroy's script
Warner Bros. deemed Wesley Strick's script too expensive and enlisted Dan Gilroy to rewrite it into something more economically feasible, with Tim Burton still attached in the director's chair. Though Gilroy did two drafts, however, Warner ultimately decided to put the film on hold due their unwillingness to fast track production due financial reasons with other film properties, leading Burton to leave for Sleepy Hollow.
In Dan Gilroy's script, the story starts with a flashback depicting Krypton about to be destroyed. As Jor-El and Lara Lor-Van place the infant Kal-El in his rocket, Brainiac enters into the room and attacks them, being behind the planet's destruction. Although Brainiac ends up murdering the couple, Jor-El is able to ignite the rocket, sending Kal-El to Earth and leading Brainiac to vow to hunt down the last Kryptonian.
In the present day, as Lex Luthor is about to discover Superman's civilian alter ego and expose it to the world, Brainiac meets Luthor. Devising a plan together to destroy Superman, the two villain merge into a single cyborg entity known as "Lexiac". They then create Doomsday, who attacks Superman until they both die. As a result, Superman's funeral is celebrated and his corpse is send to the Fortress of Solitude. However, Superman's powerless body is resurrected by the mysterious Kryptonian force known as "K", which is actually the remaining "life essence" of his biological parents.
Meanwhile, Lexiac plans to destroy the Earth much like Brainiac did with Krypton. While trying to woo a grieving Lois Lane, Lexiac assembles an arsenal of nuclear warheads to detone the world's top cities. Superman returns to Metropolis and gets his powers restored by K, allowing him to defeat Lexiac and destroy the half that contains Brainiac, bringing his threat to an end once and for all.
- When Kevin Smith was replaced by Wesley Strick as the film's writer, one of the criticisms he had against Strick's script was that Brainiac's plot to launch a disk on space to block out the sun so he could render Superman powerless was reminiscent to the two-parter The Simpsons episode "Who Shot Mr. Burns?", where Mr. Burns intended to do the same as he considered the sun to be his biggest enemy.
- Christopher Walken, Tim Burton's top choice to play Brainiac in Superman Lives, previously played Max Shreck in Batman Returns, the second and last Batman film Tim Burton directed for the 1990s Batman film series.
- Curiously, after Burton left the project to direct Sleepy Hollow, Walken was cast in that movie as the Headless Horseman.
- Although Superman Lives was ultimately scrapped, the idea to merge Lex Luthor and Brainiac into one being was eventually recycled for the DC Animated Universe show Justice League Unlimited, depicting Brainiac placing a nano-tech copy on Lex Luthor, influencing him and ultimately curing him from Kryptonite poisoning before facing the Justice League together.