The Whole Justice League are Grave Robbers
The differences that have been revealed surrounding Superman’s resurrection begin with the collection of his body. In the movie we only see Flash and Cyborg exhuming his body, with a little back and forth bonding time where they realize they’re both “the accidents,” considering the origin of their powers. While the movie makes it appear as if this is a mission mounted solely by the two youngest heroes, Zack Snyder has posted a behind the scenes image proving at least Wonder Woman and Aquaman were also meant to be present (with many assuming Batman was driving the van)
While the actual digging was likely still performed by Barry and Ray, the presence of Diana and Arthur shows there was at least more connective tissue, making the collection of Clark’s body more than just a cutaway scene, which is ironic considering Whedon’s involvement was originally cited as participating in rewrites to add connective tissue, yet that’s ultimately one of the biggest things lacking from the movie.
The Mother Box Resurrection
The actual mechanics of the resurrection were likely fairly similar, with the Mother Box acting as a sort of cosmic defibrillator, but there’s clearly a significant amount of missing context. How did they come to know that was a viable idea? Batman isn’t exactly one to say “let’s try electrocuting a dead body and see what happens?”
The most likely explanation is that the Kryptonian Codex inscribed into Kal-El’s body was somehow relevant. In interviews before the movie’s release, Ray Fisher said Cyborg has access to vast knowledge of the galaxy due to his fusion with the Mother Box, so he likely has an understanding of Kryptonian physiology and knows how to use the Mother Box to jump-start the whole resurrection process.
One of the leaked deleted scenes featured Cyborg learning the history of the mother boxes and delving into their full capabilities (which is traditionally an unlimited scope), so it only makes sense that it was him - not Batman - that came up with the idea. The fact that the dialogue with Bruce Wayne coming up with the plan is visually clearly a reshoot only supports that assertion.
Another Knightmare
Thanks to the reveal of one of Zack Snyder’s storyboards featuring Darkseid, and a little bit of context that this was a vision seen by Cyborg, we know that Superman’s return was far heavier than what happened in the movie. Thanks to some leaked pre-vis footage and behind the scenes shots, we know his initial return and fight with the League was mostly the same, with some Superman dialogue changes made evident by bad CGI mustache removal, but the League had far more reason to fear him than that.
Batman has already had one “Knightmare” where he’s killed by Superman. This new Knightmare by Cyborg has a reference that makes it in the final film when his armor freaks out at Superman and he says “it’s more powerful since the interface” (referring to his interface with the Kryptonian ship, which trigged the Knightmare. The reason his suit would react that way to Superman is because he was just exposed to a potential future where Superman killed Batman and possibly more League members.
This means the fear of Superman would go far deeper after his return. There’s clearly more missing there, as Superman’s recovery and return to good ol’ Clark (with a few more scary CGI smiles) is so truncated. With such a significant portion of Superman reshot, it’s clear his part in the movie wasn’t what Warner Bros. wanted. After both Batman and Cyborg had a dream about Superman serving Darkseid in an apocalyptic future, there was likely more mistrust and concern from the League after he ended up battling them in Metropolis.
The negative response to a conflicted Superman who has trouble gaining trust from the people of Earth - particularly Batman - was a clear influence on the reshoots, as those elements were absent from the final product, but it was a theme likely to be continued by Snyder, with the League slowly coming to trust him, eventually ending up in the same place as Whedon, only with a little more angst in the middle.
Collecting the Super Suit
We know from Flash’s cameo in Batman v Superman that Lois is “the key,” but we don’t know what Superman’s full recovery originally looked like. Joss Whedon’s final cut removed the Kent Farm scene that seems to imply some more time spent there and a much deeper conversation with Lois. Whatever happens, though, he does accept his role as a hero again and return to the fight, only he has to get his suit first.
While the movie has him simply showing up in a brand new suit, we’ve seen the deleted scenes where he returns to the Kryptonian ship to get it. While it certainly functions as a small plot hole filler, that’s not its sole purpose, as it’s also a completion of Clark’s arc, bringing him to the moment of choice where he chooses to be the bright beacon of Superman he was meant to be. Without this scene, the only thing separating him fighting the League in Heroes Park and him saving the day against Steppenwolf are a few short lines of dialogue about how Lois thinks he smells good and how coming back to life feels “itchy.”
Without the infamous Snyder Cut, it’s impossible to know exactly what all these gaps in the movie were supposed to look like, but it’s pretty easy to identify that the gaps do in fact exist. Simply extending the plot from Man of Steel and Batman v Superman to the context of the known Justice League deleted scenes reveals that a good chunk of Superman’s resurrection and return to the symbol of hope he’s supposed to be were cut and partially reshot, leaving Justice League’s Superman with a beginning and end to his story, but nothing to connect the two.
