NOTE: Snyder has stated that they will be borrowing elements from The Dark Knight Returns for the movie, so I based my treatment heavily on that storyline.
Before I begin, I must mention that Bruce is 40-years-old in The Dark Knight Rises, which takes place in 2016. I was told that Man of Steel takes place in 2013 (unsure of Superman's age), but I believe they could easily retcon that date and move the film to 2023 (read on to find out why that is necessary.) Alright, so here it is: My treatment for MoS 2, merged with Nolan's universe. Let me know what you think.
After Superman's battle with Zod, Metropolis is not only in ruins, but starting to show signs of a slow but sure nuclear winter. Analysts predict the terraforming machine caused this, and concerns are rising as the entire U.S. is slowly enveloped by the apocalypse. Looters run amok, crime is rampant, and the U.S. is struggling to hold it's image in the international scene. Lex Luthor blames this on Superman, brainwashing Americans into hating Supes, creating riots whenever he is spotted. The government tells him to lie low because of this. Meanwhile, retired, 50-year-old Bruce Wayne watches the chaos unfold in front of him.
He is forced to don the cape once again, as Robin/Nightwing/Skinny Batman (Joseph-Gorden Levitt), has formed the Teen Titans, located in Somewherefarawayland (Titans movie!). Bruce begins to restore order to Gotham. However, this awakens the Joker from a catatonic state in Arkham, as he was ever since he entered. After convincing officials he is now sane, he is released, and begins an anonymous killing spree. Batman finally meets the Joker, and after being stabbed repeatedly, is forced to break his neck. Bruce does this so he does not kill the man, but the Joker snaps his own neck, framing Batman for murder. This puts all the deaths under Batman's name, making the general public also hate and fear him (Incredibles-esque, eh?). The U.S. tasks Superman to kill the Bat. This will Rocket Supes' popularity and make him a "hero". Seeing as Supes is the governments ally, restoring the glory to him is a win for them. However, Supes is conflicted because he vowed never to kill again, but at the same time, cannot let this madman continue his rampage. Oliver Queen (Green Arrow, Stephen Amell IRL), who is a friend of Bats, warns him of the U.S.'s plans.
Bruce already has a personal distaste of Superman. In his eyes, this alien destroyed Metropolis and committed murder. He's no good. So, when Supes tries to reason with Bats in Gotham, Bruce brings along an exosuit he had been developing for years, along with other gadgets and a strange pill, to give him equal footing when he attacks Superman (THIS IS THE CLIMAX OF THE MOVIE.) Although Supes is also weak from flying through the terraforming machine in MoS 1, he still manages to overtake Batman, but just before Arrow appears and shoots him with a kryptonite-tipped arrow. However, Batman immediately dies from a heart attack, due to the exertion from his suit. Superman uses this distraction to escape. Meanwhile, a very old Lucious Fox detonates a bomb that destroys Wayne Manor and the Batcave, which was planned by him and Bruce. It then becomes public knowledge that Bruce Wanye was Batman, however all of Wayne Enterprises cash has been withdrawn and its stocks sold.
Bruce's body is claimed by a "distant relative" (Oliver Queen), and a funeral takes place, in which Clark Kent shows up. You hear a faint heartbeat, showing Clark puzzled. He then looks over to Oliver, smiles, and nods. Oliver nods back. Later that knight (haha pun), Oliver is shown digging Bruce's coffin out of the ground, and helping Bruce to his feet. He had swallowed the pill he brought to the fight, which put him into a "death state". He and Oliver walk through the tunnels beyond the Batcave, where Superman is seen standing. Cut to a scene of Luthor making a deal (Superman has joined Batman and turned evil! we must stop him) with the President and the General from the first movie, and BAM, you're set for a Justice League movie.