WARNING: The following contains spoilers for Future State: Superman of Metropolis #1, by Sean Lewis, John Timms, Gabe Eltaeb and Dave Sharpe, on sale now.
As Future State: Superman of Metropolis debuts, we get a very precarious picture of the city Superman once protected in DC's grim tomorrow. It's as dangerous as Gotham, with the U.S. government sending the army in to quell an uprising from tech-infused citizens who don't want to be oppressed by humanity anymore.
This invites Jon Kent in, the new Superman now that his dad's off-planet. But as the young Man of Steel tries to fix things, he discovers that this nightmare is actually being pushed by the new Brainiac: Brain Cells.
Brain Cells has tapped into the tech that Trojan Industries put into citizens to help them evolve. The circuitry for Brain Cells and the cyber-infusions were scraped from the skin of Brainiac after Supergirl burned the villain up for good, so Brain Cells has an easy job to tap in and corrupt the people. It's why Jon arrives to get him further away from them, so the connection gets weaker. But realizing that won't work as the army bears down to kill Brain Cells, Jon shrinks Metropolis down using the weapon Brainiac used on Kandor and flies off to the Fortress of Solitude.
There, he tries to secure the shrunken city while figuring out what to do with Brain Cells. He feels sorry for Brain Cells but the bot wants Jon to do what Superman never could: take control, not of the city alone, but the world. Little does Jon know Brain Cells has been playing him all along. He's been controlling the citizens for a while now, stirring up riots and uprisings, giving the army a reason to come. He's the one making them fire on the military and it's then and there Jon realizes the endgame. It's all to make him a villain for Kara and the army, who are both pissed at what he did to safeguard Metropolis from collateral damage.
Brain Cells simply calculated what the heroic Jon would do to reduce the loss of life, predicting the outcome would be shrinking Metropolis down. All of this would summon Supergirl to reprimand Jon, which allows Brain Cells to interface with her physiology and stirs up a brawl between the family.
By the time Jon figures out the deception and gets Supergirl back to the light after they brawl, Brain Cells -- left unattended at the Fortress -- has played his next trump card. He's kidnapped Metropolis and called down a warship, smashing Earth's drones apart, ready to finish what Brainiac started years ago. Jon's petrified as he underestimated how cerebral Brain Cells could be and now, he'll need Kara and the government to fix things and save his beloved Metropolis. It's a masterstroke that proves why anything connected to Brainiac just cannot be trusted and is best destroyed on sight.