Perhaps one of the most controversial scenes in Batman v Superman was the death of Superman. It seems a bit crazy to kill him off right before the Justice League movies, but according to Zach Snyder this was done so that Batman could be the one to bring the Justice League together. It was also done so that Superman could better relate to mankind by having a greater understanding of mortality.
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It is a very risky move for sure. Obviously killing off important characters in a movie or TV show almost always makes for a strong plot twist. The problem is that bringing them back to life almost never works out well because it weakens the credibility of the story. If one character can be resurrected, then why can't other characters that died come back to life? Needless to say, if you are going to kill off a character that isn't going to stay dead, you better have a solid plan to bring them back. Fortunately, it does appear that Zach Snyder has thought this through. In an interview with Collider Videos, Snyder suggested that the manner in which Superman is brought back occurred during his death — but was hidden from the audience.
"I’m gonna say this: the second you do the first part of it, the death and resurrection are the same thing in a weird way. You have to know. The reason I wanted to do it the way we did it is because I don’t want the audience completely off the hook with it. They still have to go like, ‘What the f**k? Are you kidding me?’.
There’s a way to signal towards a more definitive resurrection concept,
but I didn’t wanna do that because I want that to be real for them when they see it,
I want the experience to be real and then the sort of need to be real later on.
Essentially, my interpretation of what Snyder says about Superman's resurrection is that Batman v Superman hid elements of his death that are critical to bringing him back.
So with this in mind, there are two aspects of Superman's death that are a little unclear in the movie.
1. How Did Superman Die?
This one may seem obvious. In the movie, it appears that the wound in his chest from Doomsday is what killed Superman. But if you look more closely at that scene, the wound appears to just barely miss the heart (Doomsday's claw hits him from a left angle as it moves into him).
Despite having that wound in his chest, Superman was able to continue pushing the Kryptonite into Doomsday, suggesting that the wound isn't what actually killed him. My theory is that the Kryptonite blast that killed Doomsday is also what killed Superman. Watch the scene below and decide for yourself:
If that is true, than it might better explain why Superman could return from the dead when General Zod couldn't. General Zod's neck was snapped and Superman was blasted by Kryptonite. The Kryptonite didn't take the life force away from Superman, while the snapping of the neck took Zod's life away.
2. Where Is Superman's Body?
So it appears that the government had an empty coffin for Superman during the public funeral and his body was brought to the more quiet funeral held for Clark Kent. This is why the rocks and dirt were scene floating above Clark Kent's casket.
It is possible that Superman's body will be removed from Clark Kent's graveyard either because people will notice the floating dirt above his casket, or because the government was aware of where Superman's real corpse was being kept. And by the government, I mean A.R.G.U.S., which will likely have an interest in controlling and studying metahumans and aliens.
How Superman Will Return
So now that I have highlighted the two big questions that I have regarding Superman's death, I will give several theories that I have about his return.
1. Superman Will Be Resurrected By A.R.G.U.S.
The most likely scenario is that Superman never really died. He was just severely wounded by the blast from the Kryptonite and Doomsday's blow to his chest. He is in a hibernation state of sorts. A.R.G.U.S. will likely take his real body to the Kryptonian crash site where he will recover and may even be held captive by A.R.G.U.S. until events in the Justice League movie.
This would make sense for several reasons. The first is that it is similar to the comics in which Superman heals in the Fortress of Solitude following his severe wounds from Doomsday. In the DC Cinematic Universe, the Fortress of Solitude appears to be the crashed ship in Metropolis. Additionally, A.R.G.U.S. already appears to have some interest in Superman, as seen in one of the trailers for Suicide Squad in which a cabinet member asks what the government would have done if Superman had kidnapped the president from the White House:
It would make sense for A.R.G.U.S. to want to study Superman and the Kryptonian crash site that Lex Luthor used to unleash Doomsday onto Metropolis. After learning about Lex Luthor's work in the Kryptonian crash site, A.R.G.U.S. will likely try to study that area and its effects on Superman. This would almost certainly create tensions between Bruce Wayne and Amanda Waller.
Ultimately, Zach Snyder's suggestion that the death and resurrection of Superman were "really the same thing in a weird way" really leads me to suspect that his train of thought is somewhere along these lines. Superman's "death" was concocted in the Kryptonian crash site and it seems that his resurrection will come from it as well.
2. The Codex Will Bring Superman Back
One feature that greatly distinguishes Kal-El from his fellow Kryptonians that survived Krypton's destruction and also died on Earth, is that he has the Codex embedded into his cells. He has the genetic coding to all of the Kryptonian bloodlines in his cells.
Having the codex in his cells greatly distinguishes Superman from General Zod, who had his neck snapped, and the other Kryptonians that were forced back into the phantom zone, seemingly dead. It would make sense that Superman could return from the dead while they could not because of this distinction.
Under the trivia section on the DC Extended Universe Wikia's website, it stated that the Codex had been used to bring deceased Kryptonians back from the dead.
Though never stated, the Codex's capabilities resemble Kandor due to the fact that they both were used to bring deceased Kryptonians back from death and create a new Krypton
It seems as though the Codex could also be used to create Superboy, but it is unclear if Warner Bros. intends on developing the sidekicks of the Justice League outside of the dead Jason Todd and the possible appearance of Nightwing.
This is definitely a standalone possibility. But it is also somewhat likely that there could be a combination of this and Theory #1. Perhaps the Codex will be part of the reason why A.R.G.U.S. will be able to bring him back.
3. A Mother Box Will Bring Superman Back
Mother Boxes are very important objects in the DC universe. They can perform a truckload of important tasks including manipulating a being's life force to sustain it past certain injuries. In BvS it was used to bring Victor Stone back to life after a near-death experience. In the comics, it was used to heal Darksied from injuries he had following a conflict with Doomsday.
It is somewhat unclear how the Mother Boxes will work in the Cinematic Universe. They appear to be a bit larger in size than the Mother Boxes that appear in the comics. It has been suggested that Zeus brought three Mother Boxes to Earth: one was given to the humans, one to the Amazons, and one to the Atlanteans. Steppenwolf was seen showing them to Lex Luthor in the extended version of BvS, so clearly Darksied is after them. This may indicate that the Mother Boxes are more powerful and more rare in the Cinematic Universe in comparison to the comics, in which many citizens of New Genesis and Apokolips had them. If they are in fact more powerful, than it could likely be used to bring Superman back from the dead.
4. Time Travel Will Bring Superman Back
This one seems the least likely considering the dirt floating above Clark Kent's coffin, but it is certainly possible that the Flash could travel back in time and prevent Superman's death from occurring.
This seems unlikely because Snyder has said that he wants Batman to form the Justice League and if the Flash were to save him, Batman would likely know that Superman never died. But it is certainly still a possibility.
5. The Sun will Bring Him Back
There was an interesting theory mentioned in the comments section by Jim Musser. He said that he thinks the movement of the dirt near the end of BvS was the interaction between the sun and Superman's kryptonian cells.
This is a viable theory because earlier on in the movie, Superman's fight with Doomsday ended up in space where the U.S. government nuked them. Doomsday grew stronger, while Superman appeared to be near death. But then he felt the sun's rays and his damaged tissue was replenished and he was living again. That scene clearly showed that the sun can revive him.
Snyder did discuss this possibility at one point
"He comes very close to death in space and the reason why we did that is because I wanted to show — and keep the idea in the viewer’s mind – that he can come pretty close to death and the sun can revive him, or he can be revived… [But] I think something more is gonna need to be done [to revive him this time]… I felt like there’s a mythological journey for Superman. There’s the birth, death, and resurrection thing. And when you bring him back, who knows what he is when he comes back.”
How Superman Might Be Different
Zach Snyder also mentioned that Superman might be different when he comes back to life. There has been some speculation that he will return evil, maybe in a way that is similar to the Flashpoint scene in BvS which mirrored the Injusitce storyline in many ways.
It seems unlikely that Snyder would make him evil in this timeline, especially considering the fact that he hasn't even been part of the Justice League yet. So I think that one strong possibility is that he might return as just Superman and not as Clark Kent. That would be a big change with the potential to alienate many fans. However, considering Snyder's willingness to kill off Jimmy Olsen (Superman's best friend/ coworker in the comics), I think there is a strong possibility that he will no longer use his secret identity of Clark Kent after his resurrection.