Man of Steel 2.1

Clark is called by Jor- El to the field where his ship crashed. Jor- el's AI tells him he buried a piece of kryptonian technology that has great potential for mankind. The world paints the man of steel as the first wave a scout to a ailen invasion. Which was true after Zod's attack to find the codex and kill the last kryptonian on earth. Clark is still haunted by him killing Zod as superman to prevent him from hurting innocent bystanders. 
Bruce Wayne journeys to Metropolis with his secretary Barbra Gordon Aka Nightwing. Bruce dose his own investigation into Clark and discovers his secret identity as Superman and deems him as a threat to the citizens of metropolis. He confronts Clark as Batman with Nightwing at his side. Bruce reveals he knows he's superman and warns him he will do whatever it takes to kill him if he hurts innocent bystanders. And leaves after knocking him out. 
Clark wakes in his bed with Lois (Amy Adams) who says he pulled him out before the police and her father arrive. She says they call it the fight of the century between the two titans of Gotham city and Metropolis. The next night Bruce goes to a meeting with the second richest weapons manufacture in metropolis. Lex Luthor the man of the 32 century. Superman flies over on his daily routine and hears Bruce say something Batman said to him the other night. 
Superman investigates the cornfield with Lois for the piece of kryptonian technology Jor-El's AI told him about at the beginning of the movie. A surge of energy hits the cornfield and a box appears Witt Kryptonian language on it. Clark says it means the Brain Interactive Construct. Lois brought a radiation counter and says the radiation levels are off the charts. Clark takes it to the fortress to have Jor-El study it. 
Lex Luthor who says Zod and his men are the real heroes to stop the rogue Kryptonian. And attempts to get the piece of kryptonian technology Jor-El told Clark about to revive Zod and frees the rest of Zod's men with a phantom zone projector. Lex' hires John Corben his security guard who was expelled from the military and is deadly sharpshooter. Never misses his target and uses poison laced bullets. 
Jor- El tells Clark and Lois that the Brain Interactive Construct aka Brainac was lost piece of kryptonian technology that can take away a kryptonian's powers and many more. It wasn't created by Jor-El but was found by him in the caves on Earth after he saw the Kents. He took it to his lab and improved it but sent it back to earth for his son to find before he was forced to turn it into a weapon. Turning Krypton into a police state. He improved as a care package for Kryptonian's. Dating its creation back to a century before Krypton's first generation. Clark has Emil Hamilton research and tap into the box.Which he is reluctant to because he relates Brainac as the new Pandora's box. And he says he doesn't know what is inside because it's from another planet but relents after Lois threatened him with a tazer. 
John Corben and Lex's men find the fortress but find the box isn't there. But they still steal some ailen tech but Jor El's Al injures Corben as they escape. Who manages to damage the fortress console with a poison laced bullet.
Clark journeys back to the fortress with Lois, Hamilton, and Brainac. They see some one has attack the ship and stole some alien tech but figure they were after Brainac. Clark saw someone poisoned the AI who tells him it was a bullet from a military sharpshooter and goes into life support mode not before unlocking Brainac. Lex upgrades Corben with experimental bio tech and turns him into Metallo. Which cures him off his injuries and gives him all the powers Superman has. Being able to track Brainac now being 100 complete Kryptonian. 
The gang find Bruce visiting his parents gravesite in Metropolis. Superman attempts to convince Bruce to help but he refuses. Nightwing offers to join them to Bruce's disgust. Luthor vists Batman knowing he's Bruce under the cowl. He injects him with a mind control serum and sends him to help John aka Metallo. It is revealed Brainac can increase a kryptonian's powers 100%. But it would force Clark to fly into the sun afterwards draining his powers rapidly and leave him a old man. Brainac also spawns another Kryptonian named Kara. Revealing after she was critically injured she found Brainac and he absorbed her and put her on life support. Since she was on life support she looks younger than Clark. She also against the idea and takes up the moniker Supergirl. 
Batman and Metallo attack them. Metallo fights Clark while Batman fights Supergirl and Nightwing. Batman calls the Bat wing for air assault. Which knocks Nightwing out cold. Lex watches from afar with all of Zod's men and Faora. Clark activates Brainac's special ability. Solar Flare. But Brainac injects Bruce with a anti mind control serum freeing Bruce from Lex's control to Lex's Anger. Batman, Superman and Supergirl attack Metallo. While Lois calls the army to evacuate the city. Lois father is angry when Lois won't tell her why or if Superman is involved and ignores her. During the fight Batman notices Corbens body being to shake. Not being able to handle all Superman's powers with the incomplete bio tech he stole from the fortress. 
Superman attacks him and rips off the bio tech suit from Corben while Batman destroys the suit with a bat rang. Corben is taken to Arkham Asylum. Bruce secretly salvages the remains of Corbens suit to even the playground with Superman. He tells Clark he's not a menace to Metropolis and gives him a cell phone with a dark color scheme to call him for future partnerships. Lois and Clark notices their is a bat on it and laugh. Zod's men and Faora depart soon after scattering around the world to search for the Book of Rao. 
1. Kara (Supergirl) joins the kent family as Kara Kent Clark's cousin from Missouri with Lois help. And she gets a job at The Daily Planet. 
2. Clark puts Brianiac back in the fortress. And the box glows green and shows the house of el symbol on it. 
3. Lex Luthor joins Cadmus and tells Director Waller Batman is Bruce Wayne. Who smiles. Lex departs soon after waiting for future orders.