Instead of opening with the Waynes being murdered again, the movie begins with the Joker's brutal murder of Robin. Batman finds the body, tracks down the Joker and beats him nearly to death. In fact, he knocks out all of his teeth, leading to the silver grill the Joker sports in Suicide Squad.
Bruce Wayne watched the Battle of Metropolis play out pretty much as shown. He sees friends and colleagues die, once again helpless to do anything about it. In fact, it is a theme he will mention over and over. His parents. Robin. Bat Girl. Metropolis. No matter what he does, it isn't enough.
18 months later, the Batman is in the news, not for killing. He still never kills. But his methods have become more extreme. Torture and the crippling of criminals is now common and Commissioner Gordon is under intense media pressure to disavow vigilantism in Gotham.
Wayne Industries and LexCorp have formed a corporate partnership called S.T.A.R. Labs, which has won the government contract for salvaging and analyzing the alien wreckage left on Earth. They bond over their festering blame of Superman for all the death and carnage. Maybe we even give Lex a fiancee that died in the attack to ground his own rage.
Wayne and Lex get regular reports on the findings. They know what Kryptonite can do to Zod's body. However, Lex also has a private team searching the wreck in India for his own secret lab work. He discovers Kryptonite in the Indian Ocean and smuggles it back to Metropolis on his boat. He confides in Bruce Wayne that he has something special cooked up for Superman coming in. Wayne needs to know what that means.
Superman is generally going around the world and doing good, but the law of unintended consequences catches up with him when he has to rescue Lois from an African warlord. By taking out the warlord, he has created a power vacuum that has led to genocide while he plays in the tub with Lois.
Bruce continues to believe that Superman has been among us for a very long time. Much longer than the other Kryptonians. He seemed better adapted to our environment than them. That leads the world's greatest detective to start searching for Superman's real identity.
Lex uses the small sample of Kryptonite he has to remove DNA from Zod's body and gain access to the downed ship. He discovers archives within the AI construct called Brainiac (still in a mainframe form) from other worlds, including Apokalips. He learns of Darkseid and his conquest of planets. He learns the Kryptonians were able to keep him at bay by developing biological weapons that could withstand even his most potent attacks. He decides that Earth should also have such a deterrent because there is no way the Kryptonian invasion has escaped Darkseid's notice.
Bruce goes to the Lex party where he meets Clark and Diana. He is looking for Lex's surprise for Superman and hacks his files similar to the movie. Diana steals the files.
Superman is invited to S.T.A.R. Labs by Lex to evaluate the alien technology. He has agreed to help identify anything the locate and designate whether they should be safe to tamper with it further. During the meeting, Lex unveils Kryptonite, across the room. Superman is visibly shaken by it, and Lex sees this, but pretends not to notice. He also speaks of the deterrent his people had built, a sort of "Doomsday Weapon" that made them the height of galactic power. "But I guess we don't need that while you're around," he jokes.
Diana returns the files to Bruce similar to how it happened in the movie. When he sees the Meta-human files, he is visited by the time-traveling Flash (not in a dream), warning of "Invasion" and "Apocalypse". "He was right". "Lois is the key". It means nothing Wayne yet. Another file shows the Lex is smuggling the Kryptonite into Metropolis.
Batman tries to be stealthy in stealing it from LexCorp, but a highly-trained security force sounds the alarm. This becomes his big fight scene in the movie, rather than the rescue of Martha. He punches he way out and makes it to the Batmobile, leading to a high-speed chase where Batman is the one being pursued. His countermeasures eventually dispatch the security team, but then Superman appears and causes the vehicle to crash. They have their interaction similar to the movie, but Superman does use his X-Ray vision to peek through Batman's cowl. "Bruce Wayne? Final warning. Stop being the Bat." Superman departs before Batman can reach the Kryptonite has stashed away.
Later, Superman returns home and has an intimate moment with Lois. She looks at his cape and asks, "What's this?" It is a tracking device. Superman uses his super-vision to look out the window and sees Batman staring back through binoculars.
Bruce weaponizes the Kryptonite and debates whether it will be enough. He is terrified of Superman, especially now that he knows his secret identity. He decides he cannot wait for the alien to make the first move. So he sets a trap and the first part of that trap is to kidnap Lois and make her bait.
Lex grows his Doomsday deterrent in the downed ship. He is constantly overriding warnings from the AI that he should not proceed.
Superman comes home to discover Lois missing. He finds a picture of her pinned to the wall by a batarang.
Lois wakes up at the Gotham docks. She is unharmed, but the gag on her mouth prevents her from screaming. She sees Batman placing some traps and the spear. He gives a monologue about how this is where he realized he'd been too soft on criminals, that he needed to be more proactive, that he had to be more brutal to counter their escalating atrocities. This is where Robin died. When he is ready, he goes to her and says, "Don't worry. You'll be safe. But when I remove this gag, I'm going to need you to scream as loud as you can."
Superman hears Lois scream from across the bay and goes to her. Batman is waiting in his armored suit and they fight like in the movie. Lois eventually escapes her bonds after some falling debris gives her a sharp enough edge to saw away the rope around her wrists. Batman is now on top of Superman with the spear, ready to strike the lethal blow. Lois hurls herself on top of Superman, begging for mercy. Batman recalls how his mother had begged for mercy in that dark alley. It shakes him.
Lex unleashes Doomsday. It immediately escapes and starts to level Metropolis. Wonder Woman actually arrives first, but it becomes clear that she can only hope to lead the monster away from the populated areas of town. Otherwise, she is a bad-ass.
Batman and Superman hear explosions in the distance. Relenting, Batman tosses the spear into the watery hole. As his strength returns, Superman is able to use his powers to see/hear the battle in Metropolis. "It's an abomination from my world..." "Lex, what did you do?"
They join the fight and it goes down similar to the movie, except Lois is able to bring the spear back to the surface without needing rescue. She can't do anything else, though, because the battle is too far away.
Batman realizes the spear will be helpful and initiates a plan to bring the beast back to his side of the bay. US military show up but they can't do much else but keep the battle zone clear.
Eventually, the fight gets close enough for Superman to retrieve the spear, but it is clear to Lois that he can't hold it for long. She begs him not to do it, but he says he has to. The movie pretty much plays out the rest of the way as it did in Snyder's version. The only difference is that when Batman visits Lex in jail, he is a bit more explicit on who is coming. Now the Flash warning makes a bit more sense.
Batman asks Wonder Woman to help him find the others, because for all his faults, Lex was onto something. "Superman was our deterrent and with him gone, we're going to need all the help we can get".
