I can't believe this has happened. The Death & Return of Superman remains my favorite comic book story of all time and is the reason I became a hardcore Superman and DC fan. I was pissed by Superman/Doomsday (it doesn't hold up at all today) and have long dreamed of WB doing this right.
It's easy to adapt the story into two films:
Part 1 begins with a credits montage showing Superman's departure from Krypton, adoption by the Kents, debut as Superman, and revealing his ID to Lois. The movie then opens with Superman's interview with Cat Grant. The JL (mix the League at the time (Blue Beetle, Gardner as a GL, Booster) and include Flash and Batman. The rest of the JL is elsewhere and this team tries to stop the creature. Superman arrives, catches Booster, and the fight begins.
Meanwhile, Lex is watching in Metropolis (have to go with classic Lex instead of Luthor II) while Lois and Jimmy are scrambling to a helicopter to cover the action. Part of the battle has to take place over Cadmus to introduce their cloning operation for Superboy's later debut. Ma and Pa Kent are watching from Smallville, transfixed.
The battle reaches Metropolis, Superman saves Lois and Jimmy's helicopter, Clark and Lois kiss goodbye. The final fight begins as Metropolis watches on. Superman and Doomsday collide a final time and fall to the ground. Lois cradles Clark in her arms as he dies. Despite attempts by Cadmus and EMTs, Superman can't be revived. Word goes out that Superman is dead, Luthor is furious but plans to build the memorial. Ma and Pa are shown collapsing at hearing of Clark's death.
Cadmus arrives and takes Doomsday and Superman's bodies. Lois goes to Batman (he has to be in this more than the original story, unfortunately) to steal Clark's body from Cadmus. They succeed and return his body to the tomb in time for the funeral. The funeral scene has to be recreated almost entirely from the original story. The Kents, meanwhile, go to bury Clark's things and Jonathan has a heart attack. As Clark's casket is interred beneath the memorial statue, Jonathan flatlines. The funeral over, Lois gets a call from Martha about Jonathan. Jonathan finds himself in the afterlife and sees Clark at the center of the Kryptonian funeral procession. He pulls Clark out of the procession and away from the light and back toward life. Jonathan awakens in the hospital, calling out Clark's name and telling Martha "I brought Clark back to us, Ma." Lois returns to Metropolis and is called to Superman's tomb by Inspector Henderson: Superman's body is missing. End of the first movie.
Part 2 begins with Lois investigating "Superman sightings." We meet the Steel, Last Son, and Cyborg as she does, seeing each of them in action and Lois' reactions to them. Last Son and Cyborg disturb her most. Superman (not Superboy!) is waiting for her at the DP and hilarity ensues. We cut to Cyborg Superman flying Doomsday into space, chained to an asteroid. In the Fortress of Solitude, we see the source of Last Son's power: the solar matrix. A figure stirs within as we cut to an alien ship arrive over Coast City. The pods are deployed, destroying Coast City. In Metropolis, Cyborg Superman leads a press conference, announcing to the world that he, the Last Son, and the young Superman will tackle the threat in Coast City and help any survivors. The JL mobilizes to confront the ship as it returns to orbit. Once at the former site of Coast City, Cyborg Superman annihilates the Last Son and incapacitates Superboy.
The Last Son's energy form returns to the Fortress, where the robots reveal that he's the Eradicator and how he took Superman's body back to the Fortress. In the wasteland that was Coast City, Cyborg Superman and Mongul oversee the construction of Engine City while Superboy looks on. In the Fortress, a figure emerges from the solar matrix, appearing to be the Last Son in a black suit. He asks why his eyes hurt and to be shown what's happening. The robots show him Superman's battle with Doomsday, death, and the four Supermen. Determined, he tells the robots he has to get to Metropolis. Cyborg Superman launches a missile with Superboy attached toward Metropolis; Superboy uses his tactile telekinesis to escape and bring the missile down in the Atlantic. He's rescued from the ocean by Steel, who brings him to emergency personnel at Metropolis Harbor. Lois arrives to cover the story. As Superboy explains what went down in Coast City and the true intentions of the Cyborg Superman, a Kryptonian warsuit seen earlier in the Fortress. The black-clad figure emerges from the suit, claiming to be Superman. The scene where he and Lois kiss and she realizes it's him has to be there. Superman leads the Man of Steel and Superboy to Coast City, where they find a restored Eradicator. The Eradicator confirms that Superman did indeed die and joins the battle against Cyborg Superman's forces. Superman faces Cyborg Superman, who reveals himself to be Hank Henshaw and that he blames Superman for his wife's death during a botched space mission. Henshaw moves to blast Superman with the kryptonite canon, Eradicator jumps in front of Superman, and the energies are converted to yellow solar radiation, restoring Superman's powers. He defeats Henshaw with a punch to the chest/super-speed vibration.
Superman thanks Steel and Superboy for their help, with Steel asking Superboy if he's still going to call himself Superman. Superboy replies with "I'm not Superman. That guy's Superman, the one and only!"
We cut to Lois working in her apartment in Metropolis. She's writing two headlines: SUPERMAN LIVES and SUPERMAN DIES AGAIN. A tap at the window draws her attention, and she walks over and opens the window. Superman floats outside, wearing his classic uniform. Lois jumps into his arms and they kiss. They break the kiss, and Lois says, "Whew! Been awhile." They both laugh and return to kissing as we watch the happy couple and Metropolis shrink away as we leave Earth and it too shrinks away. Amidst the starlit void of space, a familiar asteroid floats by. Doomsday lifts his head up, looks into the camera, and smiles. Fade to black.
To me, these are the major beats that can and have to be hit to be faithful to the story.