Open the movie with the end of MOS, show Bruce arriving, running into the rubble, seeing Superman, glaring, basically the same thing.
OPENING TITLE.
The same terrorist situation where Lois is captured. She sees some of the terrorist figures faces. Superman, without hurting people, saves Lois, but a bomb goes off in the terrorist bunker, burning everyone completely, killing everyone inside.
Then cut to a senate hearing discussing Superman and how he still hasn't been held accountable for the destruction in Metropolis. And with the most recent unauthorized destruction of the terrorist group by Superman, as far as they think, which resulted in the deaths of 2 civilian hostages, they state that it's time they discuss what Superman should do and not what he can do.
Show Clark watching the senator talking about how they're now officially calling Superman out to answer for what he's done, for Metropolis and the deaths of those civilian hostages. He's forlorn. Lois enters their apartment, seeing him watching the senator. She tries to reassure him, telling him that he's not responsible for what happened, he just has to tell the truth. Clark says that he is. He should have seen the bomb, but he wasn't focused enough. It's his fault, it all is.
Batman is a reckless, vicious vigilante. He pummels criminals like rapists and murderers into near comas. Alfred is deeply concerned about Bruce's growing viciousness, fearful that he'll cross the line. Have the scene where Alfred says that everything's changed also have him glance at Jason's costume just as he says it. Jason's death caused him to shut down as a superhero, but after the events of MOS, he's retaken his mission harder than ever. He has nightmares about his parents deaths and Jason's death intermingling into the same event.
Superman is very much playing with kid gloves. After the events of MOS, he's afraid of his powers, the destructive force he has. He doesn't break bones, he tries to avoid destroying property. He doesn't want anyone else to get hurt. He has ptsd-esque flashbacks about the events of MOS. He still works, he's begun a relationship with Lois, which is struggling because of his disconnected attitude. Clark is obsessed with keeping himself from being something that frightens people, so much so that he's formed a partnership with Metropolis' hometown billionaire to help the city...
Lex is paranoid, rich, ruthless and fearful. He's grown and constructed his entire life around being powerful, great and untouchable. And then comes Superman, a powerful creature that is better than, more special than and more powerful than him, something that he can't control, that he can't protect himself from and he can't stand it. He's basically Batman on steroids. The Bruce Wayne worst case scenario. Only in a more self-involved way. He views Superman as a threat in waiting to him personally, not just really the world. Keep Jesse Eisenberg if you must. But make him more physically fit, not overly muscular though.
Lex's birth father abandoned him to be adopted by a broke family in the slums. He was raised by unfit parents, an alcoholic mom and a controlling dad. When they died, he worked his way through college using the insurance money from their deaths and used it to buy stock in his real father's company. When he was discovered by his dad, Lex discovered that his dad had abandoned him to see how he could thrive on his own, to see if he would ever be worthy enough for his company, then telling him that he's seen that's the case and that he's left Lcorp to him in his will. Enraged at him, his entire life being a pawn under the thumb of his real father, Lex killed him. He then used all the knowledge he'd gained to completely change the face of Lcorp, even giving his name to it, along with doing away with the oil business and making Lexcorp a science and military contract based company, creating new medicines, cutting edge research in fringe sciences, along with DNA studies, and weapons. Not to mention all of the jobs Lex created for the city after one of Metropolis' worst financial fallouts, due to the Gotham earthquake that caused significant damage to a part of Metropolis, essentially pulling the city out a kind of depression situation. Lex helped the reconstruction of the city after the battle of Metropolis as well.
Batman, after finding satellite footage from the world engine event of Superman being weakened, goes there to see if he can gather whatever weakened him, where he finds just particles, green dust left from crystalized rocks from the attempted terraforming effect of the world engine. But that's it. He investigates the area more and discovers that Lexcorp was there and took all the crystalized rocks.
Superman goes to the senate hearing where he's asked about his perception, his powers, what he plans to do about them and why he's doing what he's doing. Superman tells them that he just wants to help, that it's all he ever wanted. He's asked if he thinks the help that destroyed Metropolis by a mother of someone who was killed. Superman is visibly broken up and tries to explain that he made a mistake, he thought he could handle Zod, he didn't know it would cause as much destruction as it had.
The senators tell him that his powers aren't something that anyone can afford for him to make mistakes with. They ask him what gives him the right to do what he does when he can cause so much harm, when his mistakes do what they.
Someone tries to say that if Superman had done nothing, the world would be destroyed. Someone then yells that it's because of him that they came in the first place. The other person then yells that they don't know that for sure. A fight breaks out and Superman, worriedly starts to try and stop it, but is told by the senators that they have officials who deal with that and the fight is broken up by the guards.
Superman says that his powers give him the responsibility to try to something about what's happening in the world. They respond that responsibility doesn't give all say over the ways of the world. Superman's then asked that what makes him think that they need his help, that he has the power to fix all the problems of the world. Superman says, "Nothing. I just don't want anyone to be afraid of me anymore, when I'll I've ever wanted to do was keep as many people safe I could." They then say that he can't ever do enough.
The hearing ends, them telling him that despite the good he's done, it doesn't matter what he can do, that doesn't give him the right to act on behalf of humanity, especially if the cost of that can be the lives of innocents, and finally that they'll reconvene the next day for a complete decision. Superman leaves.
Lex uses the kryptonian ship, which was given to him as apart of his military contracts and a sample of Superman's DNA to create a clone, a mentally deficient clone, even a decaying one, something that he can control. He uses it to frame Superman for attacks. The first one being the senators from the hearing.
This shakes Superman. He sees the public and understands that no matter what he does, he won't be trusted by them, that he feels he shouldn't be, with everything he can do, everything he's done. He nearly quits because of this. It's really all about Superman's sense of inferiority. He's afraid that he can't help people now that they know he's out there. He's afraid that even though he knows the attacks happening aren't his fault he still fears that it's something he could be capable of. He doesn't see himself as helpful to the world, but as a negative force in it.
There's a running theme of a feeling of inferiority in this story. Lex feels inferior, because Superman's existence makes him feel powerless and inadequate. Batman feels helpless as ever to do good, to help people, because of such a destructive creature like Superman being around. This feeds into his already intense powerlessness at the loss of Jason Todd at the hands of the Joker due to his, as far as Batman's concerned, inaction.
Batman and Superman cross paths twice before the fight. Once during a bank robbery and another during an altercation where Superman does x-ray through Batman's cowl and tells him to stop his vigilantism. Batman rejects this and begins building his suit to combat Superman after he sees the stories about Superman's attacks, that are really Bizarro. Superman does some digging on Bruce Wayne, finding out about his parents deaths and the death of his ward, Jason Todd. He sees an escalation in Batman's viciousness ever since Jason Todd's death.
Batman breaks into Lexcorp to steal the kryptonite.
When Alfred discovers that Batman's making preparations to kill Superman, he tries to stop him, to convince him not to, that there must be an explanation for what's happening, saying that Superman has helped people and it makes no sense to turn on them now. Batman gives Alfred a version of the 1% speech, only this time citing Harvey Dent as an example of someone who wanted to help, but still turned on people. Alfred tells Bruce that if he does this, he's leaving like the others left and he's not coming back, that he can't prove 100% that it's Superman, that it could be another kryptonian come to earth. Bruce just says that the chance can't be taken. Alfred walks away.
Meanwhile Lex has been keeping tabs on Superman, tracking an energy signature that he gives off using his satellites and an understanding of kryptonian DNA that he got from breaking Zod's body down, leading him to discover his identity. Though the body is now destroyed because of the process he used to do this. He then kidnaps Martha, framing Batman for it, placing a batarang at the scene that he'd taken from Gotham police evidence lockup.
Lois investigates Superman attacks. She tracks them to Lexcorp and recognizes Lex's goons leaving the building from the opening terrorist confrontation, following them.
Superman is basically winning the fight, until he stops himself and begins to realize that he and Batman have been manipulated by Lex. Batman capitalizes on Superman's stopping and uses his kryptonite weapons. And Batman begins beating Superman brutally, mercilessly, and we see flashes before Batman's eyes of Jason Todd being beaten half to death by the Joker with the crowbar.
During the fight Alfred would try to convince Batman over the comm to stop, but Batman turns it off, saying that he has to.
He would then tell Superman that he's let too much death happen because he wouldn't do what was necessary and that he won't let that happen again. But Superman would convince Batman that he doesn't have to do this, to cross this line, that he understands how he feels. That powerlessness can make you lose sight of what's right, it can make you make mistakes, big ones that you'll regret for the rest of your life. That you can feel like you can't save anyone. That doing this will make him lose what's good in him and he might never get it back and then, confirming that he knows who he is, says, "Bruce, this isn't who you are. You can be better than this. You have to make a choice about the kinda man you wanna be. Do you want to be this?" Batman flashes back to his father telling him that in life you have to make a choice about the kinda man you wanna be. And Bruce realizes what he was about to do, what he was about to become and crumbles to the ground under the weight of that realization.
Lois tracks the goons to a building, sneaking in, where she finds Martha and unties her. She then calls Clark and tells him this and hearing the name Martha, Bruce is snapped out of his guilt stupor and realizes that he can still be a hero. Lois' then caught by Lex's men. Batman then hears from Alfred that Superman's attacking the city, or rather Bizarro is and he tells Superman. Superman isn't sure what to do and turns to Batman for help, who says that he'll go after his mom, that Martha won't die tonight, no one will.
Batman goes to Lois' location, with Alfred tracking her phone GPS. He fights the goons and saves Martha and Lois.
Superman confronts Lex and tries to make Lex stop Bizarro. Lex tells him about Bizarro with, "Aliens, metahumans, magic, it's truly bizarre times we live in. Only fair that we make something just as bizarre to combat it." He says he thought Lex was his partner, a friend. Lex tells him, "With you? After demolishing a chunk of the city, you expect any human to be a friend to those terrifying hands. The hands that'll now be responsible for the city's destruction again."
Superman, angry now, asks Lex, "Why? I only wanted to help."
"Why? Good question... Ya know, I was the hero of the city before you got here, grew up in the slums with 2 poor thugs, abandoned by my real father, and when he died I saw my opportunity to take what was rightfully mine, I pulled the city out of mediocrity and made my company and it a shining beacon for the world, then your alien invasion obliterated everything I worked for. And I put it back together again and you know who everyone cheered for? Superman. You stole everything that I earned. It's what you're here to do, take away the power human's have, decide our fate for us. To stand above us all and lord your power so we all bow down and worship you. You don't get to do that. You hold humanity's destiny in your hands and I'm taking it back. The world will look at your corpse and see you for the monster here to take our fates out of our hands that you really are. And I'll be their hero. I guess I should thank you though. You helped me see that this world was larger than I thought." Lex then snaps his fingers and Superman's tackled by Bizarro. The fight leads through the city, Bizarro trying to endanger people, Superman working extra hard to save them.
Batman hears about the fight from Alfred about and goes to help. Him and Superman together fight Bizarro. Batman using his kryptonite weapons, as Superman helps people. Batman and Superman work together to defeat Bizarro. After Bizarro is subdued, Batman's about to use his kryptonite weapon to against him, considering killing him. But Superman stops him, saying that he promised that no one would die tonight, saying that there has to be another way, that he's learned that it will only cause more pain, that this creature is just something else Lex has manipulated. Superman and Batman go to arrest Lex. Superman tells Lex he's going to make him answer for everything he's done. Lex stabs Superman in the arm and sets off a kryptonite bomb to explode and kill them, then jumping for the elevator, but Batman saves Superman, protecting him with his lead suit and the aftershock of the firey kryptonite residue hits Lex.
Aferwards Superman and Batman talk, Batman deeply apologizing for what he nearly did and Superman responding that what he nearly isn't what's important now, but we did do and what he will do. He did what was right. And that's why he knows that he can trust him. Superman decides to trust Batman with the kryptonite, saying that if anything were to happen, he now trusts him to stop him. He says that he's tried to be perfect, to be above people, but he's not and that's why he's been tormented, he's held himself to an impossible standard. He's NOT God. Not a Savior. And he has no right to allow people to think that he is. He's only human. And it's time that he accept that and start accepting help, saying that he has Batman to thank for helping him see that. Batman says that it's time he does the same.
Montage this with Lex in the hospital, the kryptonite having poisoned his DNA, making him lose his hair, it being publicly stated that there was no evidence to say he was behind Bizarro, due to the creature decaying, as all those associated with the ship defense projects are dead. And Superman confronts him, telling him that he'll put him away and accurately surmises that Lex's ego won't let him tell anyone else his secret identity. Lex himself wants the honor of destroying Superman and now Superman knows that Lex has his eyes on his family, so he'll always be prepared for him.
Then Batman comes back to the batcave to see Alfred waiting for him. He tells Alfred that he's sorry and hugs him. And he helps Bruce clean Joker's message off of Jason's costume, making it no longer a reminder of Batman's failure, but a memorial in Jason's memory. He then contacts Oracle, telling her to tell Dick that he's back. Alred, for the first time in the movie, smiles.
And Clark proposes to Lois, saying that he's ready to let her in now.
END.
Post Credits Scene is Wonder Woman informing Bruce about the coming war. Diana would still be laced throughout the movie. But more briefly. We don't even know she's WW until this moment. She breaks into Lexcorp and destroys all the files on metas, which Lex has still accumulated. After WW1, she's made herself extremely low key and protecting of the identities of other heroes and by going into Lex's files, she found out that the kryptonian ship as it was held by Lexcorp picked up an message indicating Darkseid's attack.
