This is pretty rough, but gives an idea of what I want to see
I want the film to start off with Clark trying to adjust to working at the Planet, obviously Lois and Perry are in on his secret and kind of help him to adjust to the new job. I think Jimmy Olsen should be introduced here as well. I think Clark, Jimmy and Lois should be at some event and Clark has to slip away and save the day.
It is later announced that Lex Luthor and Bruce Wayne will be rebuilding the city of Metropolis.
We cut to Bruce in the batcave. He's sitting in front of a massive bat computer, wearing his batsuit without the cowl. He's studying Superman, and says to Alfred that Bruce Wayne rebuilding Metropolis gives Batman a way to keep tabs on Superman.
Bruce arrives in Metropolis. Lex and Bruce meet, Lex shows Bruce his plans to rebuild Metropolis, and also shows him something he has discovered and been experimenting with, should Clark ever go rogue...Kryptonite. Bruce is able to get a hold of a small piece for himself.
There should be a scene of Batman spying on Superman, and then Superman can't find Batman.
The following day Bruce meets Clark and Lois at an event that announces the partnership between Lexcorp and Wayne Industries in rebuilding Metropolis. Bruce Wayne knows Clark is Superman, and Lois flirts with Bruce a little bit, making Clark jealous.
That night, Superman discovers Batman is spying once again, and they end up getting into a fight, Batman tells Superman that he's a killer and he destroyed Metropolis, and eventually Bruce gets the upper hand, he pulls out the Kryptonite and utters The Dark Knight Returns line about "remember the one man who beat you...bla bla.."
They eventually stop fighting and are able to somewhat trust each other when they figure out that they both fight for the same thing. Bruce lectures Clark over killing, and Clark explains it was the only option, and Bruce explains that with Clark's power, it's never the only option.
Bruce and Lex meet again, and Bruce starts discovering how jealous of Superman Lex is. And that his plans for the Kryptonite are much worse than he thought. Batman later comes to Lex's facility to investigate, and discovers plans to kill Superman so Lex can once again be Metropolis' favorite son.
We then see Lex meeting with Amanda Waller and a council of highly influential people in the US government. Despite Lex not being a political figure...yet...he has an incredible amount of power over the government. Lex proposes that they make Superman public enemy no 1.
Batman finds Superman to warn him, but they are ambushed by US soldiers. Batman thinks that Superman's connection to General Swanwick won't help, he thinks these orders are coming from higher up. Superman and Batman try to escape peacefully, but Superman has to destroy a tank in order to escape, and Lex records the destruction and plays it all over tv, making Clark out to be a monster. Batman is also on the tape, and he becomes a public enemy as well.
Like the public enemies story, I think Lex should offer to meet Superman, acting like he wants to make a deal. Superman would rebuild Metropolis in return for not being jailed for the destruction he caused. Batman tells Superman it's a trap, and that he won't be there to save him when it goes bad.
Superman meets Lex, and Metallo makes his first appearance, and he beats the **** out of Superman. Batman swoops in just in time to save Clark, and Bruce takes Clark to his makeshift batcave in Metropolis.
Bruce helps Clark get back on his feet, and they both realize that they are in a war against Lex and the government.
Bruce develops a plan to infiltrate Lex's facility, in an effort to get rid of the Kryptonite, but when they arrive, the Kryptonite has been moved. The facility is mostly empty, but they soon discover Metallo, who ambushes them. Clark tells Bruce that he'll take Metallo, and Bruce can find Lex.
Clark and Metallo have an epic battle, Clark is able to defeat Metallo. It's not known if he is alive or dead.
Meanwhile, Bruce finds Lex, and he gets a few punches in. Lex wipes blood from his lip and laughs, he is able to escape Bruce for a few moments and returns with Lex's power suit like in the comics. His suit is a modified version of Zod's suit. He's kicking Bruce's ass, throwing him all over the room when Clark steps in.
Clark and Lex duke it out, and Batman leaves to find evidence against Lex. He runs into Amanda Waller, who has arrived at Lex corp to take and destroy any incriminating files against Lex or the government. She tells Batman she knows who he is and that they can't be stopped. Batman is genuinely intimidated and let's her go, knowing that he's in over his head.
Clark and Lex during this fight have time to discuss their conflicting ideas, and Lex tries to seem like a good person, he feels that this is what he has to do for the safety of Metropolis.
Somehow, Batman is able to distract Lex enough for Clark to beat him.
Also I haven't figured this part out yet, but Batman and Superman's names are clear by the end of the film, and the public has no idea about Lex's villainy.
Superman and Batman shake hands at the end of the movie, solidifying that iconic friendship, and setting us up for JL
The last scene is of Lex and Amanda Waller talking about Lex's run for presidency, and how they will make it happen