In the part with Woodburn on the news, have Lois flipping through channels briefly beforehand, showing the seeds of how the world could change (for the worse) because of the Kryptonian's existence. Religious turmoil, Lexcorp weapons development, etc.
Before meeting the Kryptonians, Clark talks to Jor El, who tells him not to trust Zod. Jor El tells Clark about the codex in his blood and about how to destroy the Black Zero if and when their phantom drive is brought online. Clark seems resistant to the plan as it involves killing. Jor El also tells Clark to destroy the genesis chamber, but Clark refuses, as he holds out hope that Jor El is wrong, or that he'll be able to defeat Zod. Jor El warns Clark if he is prepared to do what is necessary when the time comes.
-When Clark meets the military, he relays the information.
-At the runway, the military refuse to hand over Superman as they all know what will happen if Zod gets his hand on the codex, and so they demand other options. The Kryptonians attack, and Superman leaps into action to save their asses. During the fight, Superman has the opportunity to kill one of the Kryptonians, but he hesitates, leading to the deaths of several soldiers. Faora ends the fight by capturing Lois, and Superman surrenders and boards their ship as a prisoner.
Act 3
-Zod speaks with Clark
-The Black Zero descends.
-Zod retrieves the Scout ship.
-Lois, using the key, breaks out and rescues Clark. They sneak around inside the Black Zero in order to escape (squeezing through many a tight space together
), but before they can escape, the world engine comes online. Lois convinces Superman to leave her so that she (with the help of Jor El) can make sure the phantom drive stays online when they bomb it, the only way to send the kryptonian army back. Superman zooms off to the world engine.
-When Supes arrives, Zod intercepts him with the Scout ship. The two battle it out with the world engine as a backdrop. When it seems like Zod has Clark beat, Clark fires his heat vision at the scout ship, the genesis chamber, distracting Zod, and Clark is able to turn the tide of the battle. When Zod attempts to kill a family, Clark reluctantly kills Zod. After a brief moment of disbelief he angrily leaps up to attempt to destroy the world engine, but he falls to the ground. He tries again, and falls. He lets out a guttural yell over this hell, having just killed and failing to save everyone around him. Cut to Metropolis, where Jenny is trapped. Clark is now crawling, almost in tears. Eventually, brief flashes of his father are triggered, then his mother, Lois, people who have shown kindness, Pete extending his hand out to him, and lastly the image of his father with his hand raised, and in a burst of effort, Clark zooms up to destroy the world engine.
-The gravity field lowers. Faora commands them to turn off the phantom drive, but it doesn't respond. Lois has done her job. In the same moment the aircraft (which has been flying way above the Black Zero all this time) bombs the Black Zero, sending the Kyptonians back. As everything from Krypton gets sucked in, the ground beneath Lois' feat dissipates and she falls, screaming.
-Superman is seemingly unconscious, but a faint echo of a scream wakes him. BOOM, off to the other side of the world. Cut back to Supes flying, back to Lois, back to Supes, etc, and he manages to catch her just in time. They fly through the air for a brief celebratory moment before they land on the Daily Planet rooftop. While Lois is overjoyed, Clark still looks distressed. "..Zod,..I..". Lois lifts his chin and directs his attention to the people below, who despite this chaos are happy that it's over, happy to be alive. Clark, having been inspired by Lois once again, thanks Lois, and he flies off. "Job's not done Ms. Lane. Just getting started here". Superman proceeds to help others in need. Folks up on buildings, a school bus full of children, etc. Fade out.
In the drone scene, the shot of the drone coming down is not so loud and kinetic, like another action scene, but rather a far away shot and a faint sound.
In the ending montage, when Clark walks in, some Daily Planet staff are fixated on the tv, where Superman had just performed some heroic deed minutes ago. Lombard makes some sarcastic remark about how they can't trust him. Jenny makes some witty comeback/insult. Perry introduces them to Clark.