Now to clairfy, the Man of Steel's story was not hidden per se, more played second fiddle compared to the introduction of The Batman to the DCCU. That's not really a bad thing, the fans just had to look beneath Bruce Wayne's captivating tale to see Superman complete his journey as a hero that was started in his solo film three years ago. Also, if you haven't seen the film, spoilers ahead, so you have been warned.
Let's start with where things picked up after Man of Steel. Clark Kent gets a job as a reporter at the Daily Planet as a cover for his work protecting Truth, Justice, and The American Way as his kryptonian alter ego. He's living with Lois Lane and doing pretty well for himself. Inevitably though, humanity questions the existence of a being they cannot control, and begin to put Superman's role as a powerful, unsupervised, international force for good, especially after the unfortunate destruction of Metropolis,under scrutiny. Now your immediate reaction would be to automatically shun these politicians who go against a superhero but to a certain extent they are right. As many people have said before, Superman in this universe is not Superman yet. Whether or not he could control how the battle with Zod was fought there a great many people in the world who distrust him for it due to the lives lost and buildings destroyed. So when Superman is once again forced to make a controversial rescue early in the movie, the resulting civilian deaths make him once again come under scrutiny.
It is now when Lex Luthor makes his move...
This...um...strange new CEO of Lexcorp automatically resents "the kryptonian" thanks to his logic of "all powerful or all good, no one can be both." Seeing the discontent and suspicion that the powers that be have for Superman, he sets him up at The Capital. Before The Man of Steel can publicly take on accountability for his actions, thousands die once again and he is not in a position to stop it.
Luthor, having created his master-weapon, now goes in for the kill. When Superman is at his lowest, he kidnaps both his mother and his best friend, finally getting his wish of coercing a god to kneel before a man. Superman has to kill Batman or he will suffer the ultimate loss. So if Luthor's plan succeeds, Superman kills the bat, giving him plenty of time to finish creating Doomsday, who kills Superman and everyone else in Metropolis except for Luthor and his minions, leaving Lex triumphant and in control of the world with a superweapon in his pocket. Say what you will about Jesse Eisenberg's spastic, mercurial portrayal of Luthor, he did have a pretty good plan compared to everything the other Luthors in the past have dreamt up.
What are bad guy didn't forsee though was the battle that followed. Obviously neither Superhero dies, Lois and Martha Kent are both saved, Wonder Woman joins the battle and the big three of the JLA take on Doomsday. As the audience expects, Metropolis is once again heavily damaged and many citizens lose their lives as the battle rages on. When the kryptonian giant knocks our hero on his butt near the end of the fight, Superman realizes what he has to do. This one action must do three things, save the world, save his friends, and clear up the doubts about this young, powerful alien's intentions for Earth. Only one thing will do the job.
So, in a beautifully shot, wonderfully dramatic, extremely emotional image, Superman stabs Doomsday with a kryptonite spear, and takes one final blow from his enemy's bony arm straight through the heart. The movie ends with both of his funerals, a quiet ceremony in Smallville for his close friends who loved him as Clark Kent, as well as a grand military funeral in Washington DC for the country that he served, as a true hero.
Now, when he inevitably is brought back from the dead to lead The Justice League against Darkseid, he will be able to come back with his held high, as The Superman we know and love. So say what you will about the movie being a "narrative mess", all you had to do was look hard enough and find a beautiful, classic story of redemption for one of America's greatest Superheroes.