It's kinda long so bear with me.
The primary antagonists would be Batman and Brainiac, but the person pulling the strings would be Lex Luthor. Lex Luthor is the penultimate rival of superman and will forever strive to destroy the image of superman before defeating the man know as superman. He would pose superman as a valid threat to the public's and the world's safety.
Batman, being the consummate detective, will investigate superman, have a bad encounter with superman due to their differing methods, and batman will have a mostly antagonistic role for half of the movie. Batman and Superman will fight, with Superman holding back considerably while noting that if he was a regular human, Batman would have certainly defeated him. Recognizing he's unable to beat Superman at the moment, Batman uses a momentary distract Superman and retreat from the battle.
Lex uses this to aid Batman portraying him as just a normal man standing up to the menace of superman. Batman would take offense to this, as Batman needs to be outside the law to truly be effective. Lex Luthor will stage a fake crime to lure batman in a meeting between the two. Lex would propose a partnership to take down superman. Batman would turn him down. Lex won't take it lightly and will try to have his men strong-arm batman, only to utterly fail and given a warning from batman.
Lex, feeling insulted by batman's refusal, stages a massive crime spree in Gotham as revenge. Batman will brought to the brink of physical and mental exhaustion trying to stop the criminals. Superman arrives to help him. Superman tells batman of his suspicions that Luthor isn't the good-hearted philanthropist the public sees him as and believes him to be behind the recent rise in Gotham and Metropolis crimes. He asks batman to help him expose Luthor. Batman says he works alone and leaves.
Lex will go to the R&D division of Lexcorp and see their progress on reverse engineering the remains of Zod's ship wreckage. They have very little knowledge of what they are seeing, but Luthor and his top scientist, Dr. Burton, have surprising knowledge of it's working from his own private studies. Dr. Burton notes that the ship has it's own form of artificial intelligence called "Brain InterActive Construct" and it seems to only respond to those of a certain level of intelligence. Luthor will be pleased by this, as it validates his intellect. Lex will tell Dr. Burton to do further testing. Burton will comply and tell Luthor that he is actually working to research the ship wireless neurological function.
Batman, while healing from his latest injuries, will have fully investigated Luthor and have found him to be crime lord on a global scale with Lexcorp as the front. Alfred and Bruce will have a talk about Superman. Alfred will stand up for the man of steel, noting that Bruce has been a man inspiring fear in the darkness for so long, he's unable to recognize that Superman is a man inspiring hope in the light. As Alfred walks away, he notes how it's a good thing to step out of the shadows and into the light once in a while. Bruce takes his words into consideration while watching shots of Superman saving people.
Back at the R&D department of Lexcorp, Dr. Burton will be recording his tests for future viewings as he attempts to link himself to the ship's "Brain InterActive Construct" and gain knowledge of it's working and it's travels, but something will go wrong and it will overload Dr. Burton's brain with the knowledge of 28 different galaxies and infecting him with some kind of organic computer virus that will slowly take him over. The ship will responds by arranging itself into a new body for Dr. Burton. The ship would then merge with Dr. Burton to create the perfect organic hybrid of machine and humanoid and will start to refer to itself as Brainiac. Brainiac will then Lexcorp's personal satellite to gain control 75 percent of the world's weaponry and electronics. Lex will find out about this and will be intrigued by Brainiac. They will have a conversation about purpose. Brainiac will muse about how his purpose was to learn everything it could as to serve its creators better, but now that his creators are gone, he will use his knowledge to help himself and that his human components have given him will and a thirst for more knowledge. He feels now that he is above all lifeforms, machine and organic, and he will learn all he can from our planet before destroying it. Lex, out of his own need for self-preservation, will offer help him to eradicate 98% of the world's population and in exchange, Brainiac will feign defeat by Luthor's hand afterwards and allow Lex to rule over the remaining human beings as part of a new world order.
Using Batman's/Waynecorp's personal satellite, Batman will be able to use his technology free of Brainiac's control and awareness. He will do his best to stop Brainiac, but will find most his attempts futile since Brainiac now exists in nearly all forms of technology. Alfred will confront Bruce about trying to do this alone and pleads with him to once in his life, admits he is only a man. Bruce accepts Alfred's counsel. Batman will find superman, accept his offer of a temporary partnership, and both will head out to stop Luthor and Brainiac before it's too late.
I wanted to an ending, but I honestly have no idea how to end it.
What's your opinion?