After I heard the announcement, I had to come up with an idea! So here it is!
The sequel will adapt loosely from the novel, The Last Days of Krypton and For The Man Who Has Everything.
Kandor, the capital and largest city on Krypton and home to General Zod. During his time on Kandor, Zod approached lead scientist, Jor-El about the future of Krypton. Both knowing the use of the planet's resources would lead to its death, they tried to make a fail-safe; a way to salvage all of krypton's history and lineage. While they failed many times, they came across an alien technology program from a planet called Colu, a planet which also suffered a similar fate as Krypton was about to. As the coluan technology seemed to survive it's planet's destruction, Zod and Jor-El believed it to be the key to help save Krypton. After many failed attempts, they unknowingly created an sentient A.I. entity, that will be known to all as "Brainiac." Brainiac, while still developing, took many of its attributes from both Zod and Jor-El, including wanting to save Krypton as well as sacrifice whatever for the greater good. However, Zod and Jor-El were convinced they failed and gave up on the project and decided to do what they could before Krypton died.
After Krypton exploded, Brainiac, surviving the explosion, was scattered across space, slowly regenerating itself. By the time it grew back to it's previous form on Krypton, Brainiac deduced that both it's creators were dead. However, having vast knowledge of Krypton, Brainiac discovered that small piece of it's creator Jor-El, still existed far off in the galaxy: Kal-El.
Brainiac makes his way towards Earth to find Kal-El. When Brainiac finally arrives to Earth, it learns that Kal-El also holds the Growth Codex of Krypton. That knowledge jump-starts the Zod personality within Brainiac, wanting to recreate Krypton, or at least his creators' home of Kandor. Brainiac's Jor-El personality sees Kal-El as its son and tries to bond with him and help him recreate their world, much like the real Zod tried to do. Kal-El, while conflicted that a part of his father lives within this Brainiac, refuses the offer. Brainiac assures him that Earth will not be harmed, as he plans to create "New Krypton" from scratch. Kal-El still refuses, claiming Earth is his home and his family. Brainiac leaves the planet and begins forming "New Krypton" in space near Earth.
Government officials on Earth begin seeing a new planet being formed nearby and begin to take action. Superman tries to reason with them, telling them about Brainiac and how he means Earth no harm. The government doesn't believe his story. Brainiac, itself, transmits a message towards the Pentagon, claiming he comes in peace and only wants to create a neighbor world to Earth, so he can still stay close to Kal-El. Pentagon retorts by saying a planet that close to Earth could cause catastrophic anomalies on Earth's atmosphere. Brainiac rebuts this by claiming he has solved that by implanting part of his programming on Earth, essentially "upgrading" its atmospheric density and even the planet's technology. The Pentagon refuses to let a alien program take over their planet's technology and atmosphere and threaten war. Brainiac simply invites Kal-El and a few government officials to New Krypton to see he means no harm. Reluctantly, the Pentagon agrees to have General Swanwick and Dr. John Henry Irons accompany Kal-El to New Krypton.
As they arrive on New Krypton, Brainiac shows Kal-El what life can be like on New Krypton via symbiotic nuero-technology done by Brainiac himself. During the illusion, Kal-El imagines what life could be with his parents and fellow kryptonians. He also catches a glimpse of young girl in his illusion, named Kara. Brainiac informs him that Kara is his cousin whom he never got to meet, but his superior kryptonian genetic coding allows him to share a bond with her regardless. However, Brainiac is surprised to know that through Kal-El, he is able to sense that his cousin Kara's genetics is still active, but dormant, leading him to believe that she may still be alive. Kal-El becomes overwhelmed with that knowledge and asks Brainiac to help him find her. Brainiac agrees after Superman agrees to allows the use of the codec inside of him and he promises to stay on New Krypton. Conflicted with the new information, Kal-El mulls it over. Swanwick quickly reminds him of Lois and who Earth needs Superman. Brainiac replies saying that Earth uses him as tool, and until recently they've only seen him as a menace. Brainiac promises him the home he's always belonged to. Swanwick continues to sway Superman to staying on Earth, claiming he has come to trust him as an ally and friend. Brainiac begins to get irritated by the general's interference and begins forcing him and Dr. Irons out of the vicinity. After being attacked, Swanwick tries to snap Superman out of his delusion and convince him Brainiac is only promising a dream, but not a true reality. He tries to convince Superman that his world is gone, and no artificial world can ever beat the real thing, despite all the bad that comes with it. Brainiac starts losing more patience and starts to get more aggressive with the General. Fearing they are in trouble, Dr. Irons decides to try out his new invention, a full-body psycho-reactive armor suit. Dr. Irons activates the suit and begins fighting back Brainiac, who in turn fights back in defense. As Dr. Irons begins fighting Brainiac, Swanwick runs over to Superman to free him from Brainiac's control. Swanwick slowly gets through to him. Just in time, as Dr. Irons, though able to damage Brainiac, proved to be no match for it. Brainiac leaves Dr. Irons unconscious, as Superman finally breaks free. Brainiac begs Superman not to make the mistake of dooming Krypton for a second time, however Superman tells him Swanwick is right and reiterates his home is Earth and not with Brainiac. Brainiac does not take the rejection well and begins attacking Superman. The battle between them causes damage to the newly created planet itself, causing it to begin imploding like the first Krypton. Superman eventually incapacitates Brainiac and before leaving the doomed planet, Dr. Irons tries to shut down Brainiac for good. Seemingly successful, Dr. Irons is brought to the scout ship along with Swanwick by Superman and escorted back to Earth.
Back on Earth, Superman says to Swanwick and Lois, who is waiting at the meet-up point, that he must go back to New Krypton and try to keep it from exploding, so Earth doesn't suffer the backlash. Swanwick jokes by asking if he plans on moving the planet out of the way. However, Dr. Irons proposes they use the phantom drive and send it to the phantom zone like they did with Zod, having learned all about it from Professor Hamilton's notes. He proposes that if he can gain access to Brainiac's internal system, he might be able to recreate a phantom zone portal and send Brainiac and the whole planet away. While initially refusing to let Dr. Irons go back, Superman reluctantly allows him to come, realizing there's no other way. Before leaving, Clark kisses Lois and promises he won't die this time, jokingly.
Superman and Dr. Irons return to New Krypton. Brainiac's artificial body is nowhere to be found. Superman urges Dr. Irons to do what he needs to do before Brainiac shows up. However, Brainiac appears on a giant screen and creates a myriad of smaller, artificial clones of himself to keep Kal-El and the doctor on the planet, so they can all die. Superman and Dr. Irons, in his battle suit, take out the clones. Superman tells Dr. Irons to create the phantom zone portal, while he keeps Brainiac distracted. However, Brainiac takes it up a notch by creating clones of General Zod and his Sword of Rao army, as well as clones of his Mom and Dad. Initially hesitant, Superman manages to see past Brainiac's trickery and defeat all the clones, just as Dr. Irons successfully opens up a portal. Superman and Dr. Irons flee as Brainiac and the planet begin getting sucked into the Phantom Zone. However, the ship they need to get back to Earth is destroyed. Dr. Irons says he was able to steal some tech from Brainiac to amalgamate the kryptonian breather technology to his suit and modify it, allowing him to breathe while traveling through space for a limited time.
Superman and Dr. Irons arrives back on Earth and given praise, with Dr. Irons earning a medal of honor. Superman goes back home to his wife, Lois and tells her how maybe they should start creating their own family. He also tells her that he learned about his cousin Kara that he never knew may still be alive somewhere and that he wants to do everything he can to find her. Lois expresses happiness and tells him that she supports him, claiming that she is her family now too. They both smile and kiss.
The scenes fades to outer space, where a tiny piece of rock with a piece of the Brainiac symbol shows a light flickering as it drifts off.
NOTE: The film will also involve another Superman villain in the beginning and cameos from other supporting characters.