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The voting for the mindwipe was massive Character Derailment for everyone involved, especially for Green Arrow, given that one of his defining character traits was his hardcore libertarian/liberal ideals as regards the rights of the individual. For that matter, it would have been more in-character for Hawkman to solve the 'What if Dr. Light comes back after our families?' problem by simply smashing his head in than it was for him to vote for double mindwipe. Not to mention that many fans were confused about Batman's attempted intervention of the mindwipe, with people thinking he was objecting to the actual mindwipe as opposed to him trying to stop the personality change (which would be more in character, but it isn't really clear, dammit Meltzer...).
The scene where Deathstroke supposedly defeats an entire Justice League lineup singlehanded, in a fight sequence that could have been designed to showcase the common pitfalls of Popularity Power. Superpowers suddenly failing to work consistently for no reason? (The Atom can and often does retain full mass when he shrinks, especially when he's going for a charging attack). Sudden outbreaks of Faux Action Girl? (Black Canary having a bag stuffed over her head after having stood still, doing absolutely nothing, for a span of time sufficient for Deathstroke beating up half the team before even getting around to her. Let us recall that Dinah has the reaction time of one of the top six martial artists in the world, and can at least temporarily incapacitate Deathstroke simply by opening her mouth and screaming.) Inexplicable outbreaks of Forgot About His Powers? Green Lantern, wearing one of the most powerful ranged weapons in the universe, instead chose to go hand-to-hand against one of the DCU's finest melee combatants?
Dinah is unable to use her scream because of a bag on her head (she's plowed through steel with that birdcall, but burlap is too much), and Kyle being taken down because Slade grabbed his arm and put it in a kind of lock. (Note that it takes truly epic overuse of the Idiot Ball for Kyle to go within reach of Deathstroke at all, seeing as how Deathstroke is one of the DCU's melee combatants, and Green Lantern is a flying energy blaster!)
Let's not forget what happened to the Flash. One of two things happened in that fight: either Deathstroke was able to swing a sword around faster than the Flash could react (which would require his hands to be moving at FTL velocities), or else Wally ran his chest directly onto the point of what to him would be a stationary object. Neither of these possibilities makes the remotest bit of sense. And before someone reminds us that Deathstroke tripped Wally while he was running during the Teen Titans era, two points: one, Wally was notably slower then, and two, it didn't make any damn sense back then either.
Jean's somehow knowing Tim Drake's secret identity, when that was information more closely held than Batman's own secret ID. Tim didn't even tell Oracle who he was until several years after his career started. Tim has chosen to let romantic relationships and even his Young Justice membership entirely collapse rather than violate secret ID security. Steph had to find out who Robin was from Batman, not him, and Tim was so incensed over that breach of security that he temporarily quit working for Batman! The point is, Tim Drake is the only person in the DCU whose own secret identity paranoia makes Bruce Wayne look open and trusting, so how in the name of Rao did Jean Loring ever find out?
Both Tim Drake and his ID paranoia are products of a bygone age that unofficially ended with Identity Crisis. In the Silver Age, it seemed like just about every good guy in a costume seemed to know that Bruce Wayne is Batman and Clark Kent is Superman, but after Crisis on Infinite Earths, DC made Retcons that drastically scaled back the number of heroes who knew their IDs. Now, just like most people in the DC Universe, most superheroes didn't know who they really were. When a superhero did learn either of their IDs (whether because like Tim Drake, they figured it out, or because either Bats or Supes told them) it was always a semi-major event during that period. Identity Crisis was the first story since COIE to restore the Silver Age status quo of most superheroes knowing Bats & Supes' IDs. This was more or less revealed in the first issue of IdC when Oliver Queen, who had never been part of the "entrusted few" after COIE, kept casually referring to Superman and Batman as Clark and Bruce. Of course, since Tim Drake came on the scene long after Ray and Jean divorced, and since until IdC, he was not an orphan living with Bruce, this revision still doesn't explain how Jean knew Tim Drake was Robin. Even knowing Bruce is Batman wouldn't make it a foregone conclusion that Tim is the current Robin. To say nothing of the fact that IdC, the first story since COIE to do away with the notion that most superheroes don't know Bats & Supes' IDs, illustrated all too painfully well just why that post-Crisis revision was such a bloody good idea!
The fact that this story made that revision seem like a good idea is in itself horrible in that, Pre Crisis, the League was much like a police agency where the heroes got along well. In an Alan Moore penned story for Swamp Thing that featured the League, they referred to each other by name, making them seem more (ironically as it sounds) human and friendlier to each other (always referring each other as their hero names always seems like a weird idea, especially if they were supposed to have worked together for years).
Jean's motive for the whole plot to begin with. Jean & Ray split up the last time because she wanted to leave, and Ray didn't want her to go. The only thing she'd have needed to do to rekindle their relationship was go back and ask him for a date.
To say nothing of how ludicrous Jean's claim was that she'd not intended to kill Sue, but lugged along a flamethrower anyway.
The rape. Just... the rape. There are actually several mutually reinforcing reasons just why the rape was such a deeply polarizing event for many readers, particularly older ones.
The rape was a flashback to many years earlier during the Satellite era of the Justice League, roughly halfway through Sue's career in comics. The problem is, though, that Sue turned up in plenty of comics since then, without any hint of having suffered such a severe, life-changing trauma as a rape. If anything, she'd actually been more prominent during this second half of her career than she'd been in her first, as a regular supporting character in the short-lived Detroit version of the League, the longer lasting Justice League Europe, and in James Robinson's Starman series. In all three series (and in every other post-Satellite League comic she'd been in, including IdC # 1), she kept right on being a friendly, cheerful, happy, Lighter and Softer, Fun Personified character. In the JLE, she even worked alongside a teammate, the second Dr. Light, who had the same code name as her rapist without batting an eyelash.
The flashback was shown after she'd already been killed off, making it painfully clear that Meltzer had no interest in exploring how this rape had affected her, or how she managed to cope with such a horrific event.
In the end, the rape turned out to have absolutely nothing whatsoever to do with her murder. For all the controversy and shameless hype the rape aroused, it turned out to have about as much importance to the rest of the mini-series as a Big Lipped Alligator Moment, including the fact that it was never mentioned again after issue # 2 (the issue in which it was shown).
All of the female characters portrayed are voiceless, sometimes faceless (Wonder Woman shows up for several pages in the fourth issue, but only her hip was visible), and, above all else, victims. Sue Dibny is killed, then raped, Dinah's head is shoved in a bag, Zatanna spends the Deathstroke fight vomiting, and Jean is, of course, crazy. Which is treated, without any explanation, as a substitute for a motive.
The retool of Dr. Light. Making him re-Take A Level In Badass who could fight the entire Teen Titans roster was fine, but DC managed to make him more of a joke than he already was. Nearly every single appearance of him since Identity Crisis has him mention rape in every sentence he says. Wanting to point out the Justice League mindwiped him? "They raped my mind!" Wanting to point out how good power is? "It's like rape!" Dr. Light has become such a joke in this manner, Plastic Man even mentioned, "It's like his superpower now." It's gotten to a point where he could just be named Dr. Rape or Rapeman or Rape Ape.
So we have a civilian as the only person on the Watchtower? Um, who the heck thought this was a good idea? First off, these heroes basically protect the entire planet, right? Natural disasters don't wait for the standard working hours of Metropolis (or whatever timezone the Watchtower is set to). It's always daytime somewhere, so there should be a minimum compliment of heroes up there at all times, or at least someone to keep the civilian away from the dangerous stuff!
That's a wall banger that stems from the writer not doing the research, and of an era of comics he was supposedly a fan of! During the Satellite Era of the Justice League there WAS always at least one JLA member on board the satellite at all times. It was called "24 hour monitor duty" and every member took rotating shifts on it. Not only should there have been at least one superhero on board with Sue at the time Dr. Light broke in, but there would have been if the flashback had been from an actual Seventies comic. But there isn't for no other reason than because DC "needed" a rape.
After Atom finds out his ex was responsible for Sue Dibny's death because she wanted him to come running back to her, why does he commit her to Arkham asylum of all places!? Not only is that place hardly conductive to one's mental health, but the place also happens to hold 51% of all psychotic super villains at any given time, but she's also publicly known as the Atom's ex-wife! Either the Atom is a phenomenal idiot, or he's just that cold. Besides which, Arkham is an asylum for Gotham City, a place in which Jean Loring has never resided. There aren't any mental institutions in Ivy Town?
Worse still, Sue knows that Bruce Wayne is Batman. Arkham houses 90% of the guy's enemies! Even if they didn't think she knew, she's batshit insane! She could let it slip at any moment, and thus Bruce can be targeted by his enemies. This makes it less about Sue's well being and more about the phenomenal idiocy in regards to Batman!
It gets revealed at the end that the burning of Sue Dibny's body was done by Jean with a flamethrower to conceal the real cause of death, stroke. But then Ralph Dibny and the others immediately assume that Dr. Light (the evil one) was responsible, and that he burned her to death with his light powers. Except a flamethrower shoots a burning liquid (generally a petrochemical) that would have left an obvious residue at the crime scene, whereas a flash-burn from a high intensity beam of light would not. In short, the smell alone would probably exculpate Dr. Light immediately, but the detailed examination of the crime scene we see the heroes perform would definitely uncover accelerant residue. They finally do discover that it wasn't Dr. Light when Dr. Midnite, performing the autopsy, finds that Sue's lungs are clean, showing no signs of smoke inhalation, supposedly demonstrating that she wasn't burned to death. The problem is that when you are burned to death, whether by being shot with a flamethrower or especially by being flash-burned by radiation, you don't inhale any smoke; you burn to death too quickly. People who die in building fires have smoke in their lungs typically because that's what they actually die from: smoke inhalation, not burning. Thirdly, as stated above, it is ultimately revealed that Sue Dibny was killed by what was, essentially, a stroke: Jean Loring used one of the Atom's shrinking suits to shrink down inside Sue's brain and then increase in size enough to kill her. This is eventually revealed when Dr. Midnite finds Jean's footprints on Sue's brain. Really? A trained pathologist would not have been able to determine stroke as the cause of death sooner? Strokes have highly recognizable symptoms, even allowing for the burns inflicted post-mortem. In short, the whole story makes no sense.
Let's ignore the atrociously bad science mentioned above for the moment and grant the story the premise that "no smoke in lungs=didn't die in fire". Even then, Dr. Mid-Nite's next statement, "It means Dr. Light didn't kill her!" still makes no freaking sense. Mid-Nite wasn't a part of the Satellite League at the time and isn't present to hear about the rape/mindwipe, being busy with the autopsy, and thus would have no idea why they think Light's her killer in the first place. In the second place, he still didn't know at this point what Sue had actually died from. The ONLY thing he knew at this point was that Sue didn't die in the fire. That doesn't clear Dr. Light or anybody else.
The incarnation of the Justice League with which Sue Dibny was by far the most deeply involved, one she worked for, in fact, was the JLE, hands down (Green Arrow even points this out in his narration!). Yet other than Ralph Dibny (obviously) and Wally West, both of whom were in other versions of the League also, we barely see any of the other JLE members in the story, and none of them have major roles. So Green Arrow, who, as far as I can determine, barely knew Sue, narrates most of the story, but Captain Atom, who was one of her best friends for years, gets one appearance and no lines. Likewise for Power Girl. Rocket Red (unless he's the guy at the very back at the funeral, out of uniform), Blue Jay and Metamorpho didn't even get that.
Sue's death occurred in Opal City, and towards the end of Robinson's STARMAN run she and Ralph had met and worked with the Shade, who quite liked them. Given Richard Swift's historical response (hint: it involves murder) when someone, especially some out-of-towner intruding in his city, targets anybody he's personally fond of, you wonder where he was during all this. Of course, given the quality of the writing, he was personally better off staying the hell away from this crazy plot.
Elongated Man, Batman and numerous other detectives are involved in this story, yet none of the detective work proceeds as a real case would. As we see, anyone can set a fire with a few simple tools or weapons, but all of the super-heroes race off to find fire-based villains regardless of how tangentially (or not-at-all) they know Sue Dibny. Later, just to drive the point home, Jean is attacked with rope (attached using a standard knot), so they interrogate Slipknot even though he is in jail, cannot tie a rope now that he has only one arm, and has never met Jean or Sue.
There is no mention of Sue Dibny's actual arch-enemy, Sonar! In the Elongated Man mini-series, she encourages the nation of Modora to overthrow Sonar (Bito Wladon). Later, in Justice League Europe, he conquers the entire fallen Soviet Union and parts of Europe. However, this scheme entirely fails because he had tried to woo Sue away from Ralph and she played him for a sucker. The guy could have been the next Napoleon, except for Sue Dibny. Sonar should have been the likeliest suspect, even with the rape by Dr. Light.
Ralph Dibny never questioned what happened to Dr. Light until they are outside his apartment? Really?
Suppose Ralph and Sue had come back from the hospital ready to go public (as is their nature) with this crime? How can they prosecute Dr. Light in court for rape if the Justice League has mind-wiped him? Why is all this done without even consulting the victims about their intentions?
How likely is it that Black Canary, an outspoken feminist, would be voting to protect Dr. Light for raping her friend? (This is later referenced in a Justice League of America issue.)
Why is Batman going on about the 'who benefits?' thing when his own enemies mostly commit crimes with no tangible benefit? Murder for the sake of murder should not be a new idea to him.
Hell, his most famous enemy is the friggin' Joker! Whose motives for anything he does is either For the Evulz or for the lols. Batman's tangled with someone who is inarguably the DCU's biggest psychopath for years now, so this shouldn't be anything new to him!
A standard procedure in any murder case is to check the victim's phone records. If the superheroes had done that, they would've noticed that Sue received a phone call just seconds before her final, frantic phone call to Ralph (that call is how Jean got into her home and entered Sue's brain using Ray's Atom powers). If Jean left the same way she got in, then she would've had to use Sue's phone to dial back to wherever she called from. That's 3 quick phone calls on Sue's phone at the time of her death and only the second one (Sue's call to Ralph) is accounted for, a fact that should've loomed large in any real life investigation. If Jean were dumb enough to call from her cellphone, home, or workplace, then the "mystery" would've been solved by the end of the first issue. If she were a bit smarter and say, used someone else's phone, that might've delayed the investigation a bit longer with initial suspicion falling on Ray before they realize it's Jean. In either case, the investigation shouldn't have lasted for 7 extra long issues.
Ralph states that to keep Sue safe, he has monitored his home with all the best technology from Krypton, Mars, and Thanagar. Even granting that all that security wouldn't detect Jean's microscopic presence, in issue # 1, we see a normal sized figure setting fire to Sue's body. This is reinforced in issue # 7 with a flashback to that moment revealing it's Jean, indicating she grew to full size to set fire to Sue... and all that Kryptonian/Martian/Thanagarian technology didn't go off even then?!?
There are so many bad red herrings that exist in this story that are completely inconsistant with the final solution.
In issue # 1, Sue hears a *thump* in the basement and goes to see if it's Ralph back home early. This is not how Jean came in. This discrepancy was remedied with an Author's Saving Throw in the 52 maxi-series. But there are others...
In issue # 1 at the time of Sue's murder we see her flying across the room as if someone had just punched or thrown her with great force even though we later learn that all that actually happened was that she got a literally killer headache.
When Hal Jordan shows up as the Spectre, he says of the killer, "Make them pay," which suggests that Sue's murder was some kind of conspiracy. It isn't. He said "them" solely because it's gender neutral. If he'd said "Make him pay", he'd wind up looking less than omniscient which would be a real problem what with Hal being a part of an aspect of God and all. If he'd said "Make her pay," every reader would instantly know Jean was the killer since she'd been the only woman in this damn thing to have more than 5 lines of dialogue. So he says "Make them pay," and still comes across as somewhat less than divinely omniscient.
But the worst would have to be at the end of issue # 6, when suspicion starts to fall on Ray Palmer. The final scene of that issue shows Ray alone with Jean, and he has this really creepy, sinister, evil-looking grin on his face. Jean even asks him to stop grinning like that! Why is he grinning like a psycho? Because Meltzer wants to fool you into thinking he's the killer when he isn't. THERE'S NO OTHER BLOODY REASON FOR IT!!!
At one point, it's revealed that Sue was pregnant at the time of her death. One problem with that: Ralph Dibney gained the powers of the Elongated Man from a solution called Gingold. One of the side effects of Gingold? Sterility!
Seeing as Meltzer's grasp on the Silver Age is tenuous at best, one could assume he simply didn't know. Otherwise, it would imply that Sue had cheated on Ralph (unless they were trying other methods like a donor, it was never explained) which does not seem bloody likely at all and would be yet another derailment of Sue, this time of her very character. Sue and Ralph were devoted to each other and part of a committed relationship. Which was probably why it had to be broken in the most cruel, heartbreaking manner and with extreme, violent, and utterly brutal prejudice. Even if Meltzer genuinely didn't know about Gingold making one sterile, it doesn't matter because the pregnancy itself was meant to add more shock value to Sue's death.