^I love a good redemption movie. How would you incorporate Brainiac into the movie's themes?
I would go for Metallo, with him being a soldier that was put out of commission by collateral damage from Superman's attack on the warlord from BvS. The man backing Metallo would be an up and coming tyrant that stepped in to fill the power vacuum Superman created when he killed the warlord. Metallo would be used to consolidate the new tyrant's power in Africa, along with the acquisition of various bioweapons, you know, dirty bombs and the like. Superman would try to defeat Metallo by talking him down rather than engaging in battle; this would prove ineffective, costly, and force Superman to find a way to fight this villain while minimizing the damage to Metropolis and wherever else they fight.
I would tie this into the idea that Clark Kent might be able to do just as much good for Metropolis and the world at large as Superman - let good investigative journalism rattle the cages of the movers and shakers to deal with the world's evils. Like, a hard-hitting piece on the tyrant's rise in Africa may have prompted intervention before Metallo's creation, allowing the soldier that would become Metallo to get the kind of physical and psychological treatments he'd need for his maiming. This would let us move toward a Clark Kent that still works for the Planet and a Superman that can be deployed when journalism fails.
Man of Steel III: In Fires Forged
This is the film where I'd use Brainiac. I would cast Brainiac as an extremely intelligent extraterrestrial that once ruled an entire planet. He lost that planet to Mongol and intends to get revenge on Mongol.
Clark Kent and Lois Lane are investigating a human trafficking ring run by a man who should be dead - Anatoli Knyazev. Both of them get a demonstration of KGBeast's new abilities when one of his men, evidently horrified by what he's seen of KGBeast's new customers. At that moment, one of the customers appears - an extraterrestrial by name of Mongol. Clark is hesitant to spring into action, fearing for the innocents being sold off to Mongol. During the exchange, Clark hears something about the deposed ruler Brainiac.
Lois runs the story on the trafficking ring while Clark digs into his Kryptonian lore to see if he can find any references to a being named "Brainiac." He discovers that Brainiac - a once benevolent ruler - was usurped by his second-in-command, Mongol, when Brainiac's benevolence left his home plane vulnerable to its own criminal element. According to the archives, when the criminal elements rose up and began seizing the planet from its lawful rulers, Mongol usurped Brainiac and became the planet's first military dictator.
Brainiac attacks Earth with the intent of scavenging the remains of Zod's terraforming machine; Superman fails to prevent the attack - Brainiac's forces are extremely zealous in their devotion to the deposed ruler, and strangely it seems that they're taking care to do as little damage as possible while taking the terraforming machine. Superman thus pulls back with the intent of following Brainiac to see what the ex-ruler plans.
On Earth, Lois draws the ire of KGBeast and his gang. So, KGBeast decides to make Lois disappear by offering her up to Mongol and his men.
Superman arrives to see Brainiac using the terraformer to seize a dying planet. The terraformer allows Brainiac to turn the planet into warworld. Brainiac, with his warworld, sets a course for Mongol with the intent of raining fire and death down on the usurper and the planet that, Brainiac believes, betrayed him.
Lois escapes her captors on Mongol's prison planet and uses her skills to drum up a resistance to Mongol. She argues that the usurper's privations will create more of the criminals that he sought to eradicate. Lois's resistance gets a look at what Mongol's been doing with the humans he obtained from KGBeast - they're being used as bioweapons, for the usurper admires the human propensity for cruelty, unpredictability, and the malleability of the human mind.
Superman is forced to intervene in the war between Mongol and Brainiac by battling Brainiac while Lois deals with Mongol by raising the oppressed against him.
Edit:
I was looking up Brainiac and saw that he was originally a ruler that lost his planet. It looked like an interesting angle to explore, one that you don't often hear in fanscripts. I decided to take that, and included Mongol for some parallels between the conflict between Batman and Superman in BvS.