Zatanna erased Sue's memory of the rape
Explains why such a traumatic event never came into play before this story. The ending of Identity Crisis wasn't decided until sometime during the writing of the second-to-last issue.
The outcome of the story makes no sense given the facts established earlier on. The flamethrower comes to mind. The surprise twist at the end was most likely mandated by the editors for some nefarious purpose, possibly to set up Countdown.- The Countdown part is not freaking likely since Countdown wasn't even a twinkle in Dan Didio's eye when Id.C. was being written. The part about Brad Meltzer not knowing who the hell the true criminal was until the end, DOES seem to fit very, almost uncomfortably, well.
- More likely, they did know who the true criminal was, but it was originally planned to be someone else...
The original choice for the true killer was...
- Someone planning to put Dr. Light back in business
- Superboy Prime (or perhaps Kal-L)
- Heat vision of the silver age variety might not leave trace evidence, and silver age super-speed was certainly capable of Flash-like vibration through solid matter. Silver Age Superman once even traveled to the future that way.
- This story predates Infinite Crisis. So this is pretty much not possible.
- Except everything the writers have said about Infinite Crisis has mentioned that it was being planned as far back as Teen Titans/Young Justice: Graduation Day, a while before Identity Crisis (2004) came out.
- Heat vision of the silver age variety might not leave trace evidence, and silver age super-speed was certainly capable of Flash-like vibration through solid matter. Silver Age Superman once even traveled to the future that way.
- Mr. Mxyzptlk from Whatever Happened to the Man of Tomorrow? continuity. Somehow Crisis on Infinite Earths brought him back to life and allowed him to sneak into the single Earth created. He has been slowing picking apart this universe by causing events that do not have rational causes or outcomes. His plans nearly came to fruition with Final Crisis but the superheroes just barely managed to stop him. For now.
- Ray Palmer. Seriously - go read the book again and think about how much more sense everything makes with the original Atom as the killer; Jean, for instance, has seemingly no interest in getting back together with Ray until the final issue; she also manages to hang herself in an extremely unlikely fashion at her own home which would be under the same manner of protection as the Dibny residence, and she also has someone attack Tim Drake, which makes no sense whatsoever as she hadn't maintained the same connections to the superheroes that others had; Ray, on the other hand, had distinct knowledge of how his size-shifting abilities could work and could be used to hurt someone (and later uses them in the same way Jean did in Cry For Justice), knows the League's security measures (and is shown working through carpet fibers so he could hide his own evidence), knows about villains like Slipknot, and just so manages to turn up in time to save her life when she's being hung? All the facts when reading the book point to Ray as a more likely candidate for the killer than Jean.
- This actually makes a lot of sense — there's a parallel WMG regarding Blackest Night regarding Ray Palmer joining the Indigo Tribe, who are well–known (but were not at the time) to only accept sociopaths as members, with the intent to redeem them by force–feeding them compassion. This would also explain Ray's frankly odd choice of weapon with which Jean could defend herself (a medieval crossbow? Not even a modern, hunting crossbow?), since he knew she was in no real danger and he could afford to come off as a lovable doof (who even has a medieval crossbow? You're a physicist, Ray. What'd you do, steal it from the history department?) without it endangering her. This also means that his Wham Line, "How'd you know about the note?", is born from actual confusion rather than him catching her in a lie. Her mental breakdown could be because she saw him writing the note, figured out he was the killer and that it was because of her, and had a breakdown while trying to cover for him.
- The change was made at the last second when DC decided it didn't want one of its main characters and all-time Justice Leaguers being a villain.
- I KNOW WHO IT WAS SUPPOSED TO BE!! IT WAS CAPTAIN ATOM!! But then readers figured out the mystery too early, so a C-List supporting character was set up to be Extant... I mean the killer...!
That wasn't a flamethrower that Jean was packing...
...It was a fire blower which shot fire from the fire dimension! Because real flamethrowers use a petrol compound to burn, and there would have been trace evidence. This is the only way to explain why the Cabal could have possibly thought that Dr. Light was the true killer since a flamethrower absolutely does not fit Light's MO. ...Well that or Brad Meltzer is a bad fucking writer, BUT STILL! And I swear to God, NO FREAKING SUPERBOY-PRIME PUNCH JOKES; IT'S GOTTEN OLD!- Maybe it was a modified gadget of the Atom. That's probably how Jean easily shrunk it down to being along with.
- It was the Scarlet Witch saying, "No more trace evidence..."
The fight with Deathstroke went differently, the version we see is the one the superheroes have agreed to tell because the truth is too embarrassing
When they saw Deathstroke willing to fight a lineup of the Justice League they doubled down in laughter, and Deathstroke, not being an idiot, bashed them on their heads until Green Arrow punched him in the balls. After that they agreed to the story and altered Deathstroke's memory to fit it.