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The mass-deroboticization wouldn't work on Bunnie because she upgraded her robotic parts and they were not her original limbs; but it could work on Eggman and Snivley, who we know had their minds transferred to at least two bodies, neither of which were their original roboticized forms. This has never been explained.
The implication is that since Bunnie's limbs, built by Nate Morgan, were more traditional cyborg limbs, while Eggman & Snively presumably had their new bodies built from scratch using the roboticizer, making them fair game for the alien intervention. She would later get her limbs turned to flesh & blood by Naugus much later (though even he didn't know how at the time, presumably due to his Chaos Emerald). Any future ideas for what she would do then (which implied her being so shook up that she wasn't able to save Antoine, she'd try to get her uncle to Legionize her to get her limbs back) was then scrapped by the Penders-lawsuit-induced reboot, where her limbs were explicitly said to have been given to her by Uncle Chuck to save her life during Robotnik's initial attack.
The "25 Years Later" What If? storyline, which started promisingly with the discovery that the heroes' constant use of Chaos energy threatened to destroy the planet, but then degenerated into ten issues of Sonic and Knuckles talking about family life while their wives and daughters spent an entire installment at a slumber party and ended in an infuriating Anticlimax. Ian Flynn later followed it up with a continuation of 25YL (which was just as bad as the original) and a sequel arc called "30 Years Later" (which was so bad even Flynn himself considers it an Old Shame).
Shadow, a villain in the 25/30YL timeframe, gets easily frozen by Chaos Control from Knuckles' daughter despite Shadow's having direct control over the primordial forces of Chaos itself in the universe without the need for a Chaos Emerald and her being an amateur teenager with no combat experience.
The Word of Gay concerning Rotor is a major Wall Banger, in and of itself. Originally, it was meant to give the walrus some much-needed Character Development to offset his perpetual Demoted to Extra status; but suddenly making an underused character a Token Minority for "character development" is not only lazy and stupid, but also offensive to that minority (especially when the Word of God also claims it was to explain away his social awkwardness. Hey, Ken, gays aren't all social misfits!). Also, making a chubby Non-Action GuyHollywood Geek a Pet Homosexual raises a host of Unfortunate Implications about geeks in general and Sonic fans in particular. This could have been mitigated with deeper exploration in a future story... except there's a lot of Flip Flop of God going on with it; everything from whether Sega and Archie were on board with the it, whether it would actually be explored in the comic at all, or even what the backstory for the Word entailed.
Even worse, Ian Flynn's attempt to rectify this by declaring the whole thing "irrelevant", combined with his treatment of the duo as mentioned above, has given some readers the idea that he hated the pairing for what it was. Whether or not this is true, it seems like neither writer can do anything with the Word that won't screw it over. Though the real blame goes to Penders; according to Flynn, he had no idea Rotor and Cobar were meant to be a couple until after Penders had left the book.
Knuckles' dad, Locke, is dying of cancer. How did he get the cancer? Word of God says he got it from the genetic engineering he performed on himself to make Knuckles superhuman (super-echidnian?) interacting badly with the radiation from the Master Emerald. So why didn't the same thing happen to Knuckles. (Of course, the truth is that Penders wrote the story as a tribute to his father, but that doesn't excuse the gap in logic it caused.)
More problems from the comic post-issue 200:
Snivley hands his newly acquired power over the Eggman Empire to the Iron Queen. Granted, they're in love and plan on ruling the empire together; but so far, he seems to be perfectly comfortable as her second in command, the same position he had under Eggman's rule. Worse is that recent issues have shied away from the "We Can Rule Together" plot, booting Snivley back to abused flunky status. This is so obvious that it was Lampshaded in-comic; when Snivley tells his (mentally-insane) uncle about how he found love with Regina, the fat man laughed at him and told him Regina was using him to gain more power and vice-versa.
It can be inferred that Snively didn't mind being the Iron Queen's #2 given that she actually did give him more respect than his uncle ever did, which is why he betrayed him... twice (during Endgame, where Robotnik Prime was annihilated, and after Eggman finally went crazy).
There's also Espio's Face-Heel Turn; there had been no indication that he had allied himself with any ninja clan prior to this arc (in fact, none of the ninja clans in question were even mentioned until the arc started); yet, once it's learned that the Iron Queen had united all the clans under her, Espio is forced to work for her simply because he's now a ninja. Even worse, his first assignment is to hunt down and kill Knuckles and steal the Master Emerald. True, he eventually aborts it...but only after he's got Knuckles, his best friend and closest ally, by the throat at kunai-point. My Master, Right or Wrong should not work that way! Goodnight! Besides, having the only Freedom Fighter ally with ninja training train the others in how to fend off no less than four ninja armies would've made more sense.
Later given justification when it turns out that the Shinobi Clan's Bride is his own mother, and that his main assignment was to watch Knuckles. Not only do you NOT mess with your own mother, she made sure that it was actually impossible for Espio to kill Knuckles as it contradicted what he had been assigned to do in the first place.
Finally, when Espio's deception is finally revealed, the Chaotix are less appalled by the fact that he betrayed them to the enemy than the fact that he was spying on them. Yeah, finding out embarrassing secrets about your teammates is much more detrimental to your friendship than actively working against them and trying to kill them on orders from the enemy.
For the queen mother of all Wall Bangers in the Archie Sonic comics, look no further to the main storyline of issue #108: thanks to a machine he built and the residual effects of Chaos Knuckles' unintentional reality-warping powers, Eggman (then still robotic and able to roboticize people by touch) finds a way to reconstitute the original Robotnik. Surely, something so groundshaking, something so unexpected, something so epic simply couldn't be ruined, right? Somehow, it could, and it was. Instead of using their combined 600 IQ to come up with some mass-roboticization machine or plot out the location of Knothole for a surprise attack, they decide to indulge in an Idiot Plot involving Robotnik "escaping" from Eggman and gaining the Freedom Fighters' trust, so he can eventually lure them to the machine that brought him back, and use it to disintegrate them. Unexpectedly, and defying all logic (this is Robotnik, after all), their ploy works; for the next month, the Freedom Fighters give Robotnik shelter in Knothole itself, with both parties completely ignoring that having Robotnik in Knothole is a serious security risk, because he could relay not only the village's location, but also its defensive capabilities and weak points back to Eggman! None of the Freedom Fighters seem to realize this, and it's heavily implied in future comics that this breach in security never happened. Robotnik is eventually able to go into the machine and have it turned on on them.... but it's okay; the Freedom Fighters already knew what Robotnik was up to, something that he and Eggman should have seen coming when they formed the plan in the first place, and they only went along with it so they could destroy the machine. It was established earlier that the process that brought Robotnik back was only temporary; he only had about a month to live... which makes one wonder why they even went along with the plan if they knew about the machine when we've seen, several times before and afterward, that they're capable of sneaking into Eggman's base and sabotaging his machines, without having to resort to playing the villain's game. It also makes one wonder if Eggman knew about the revival being temporary, and why he didn't offer to roboticize Robotnik as a safety precaution. The worst part of this whole mess? It all happened in a single half issue, not even taking up that much of the comic it was featured in (the other pages being reserved for shoehorned Knuckles and Sally-centric stories), and it was never referenced again in the comics. What could've been the most epic turning point in the entire comic ended up being reduced to a half-issue, pissing on the grave of the legacy of the comic series in general, and its depiction of Robotnik in particular.
Eggman gets a whopper of a Wall Banger in issue #210. After he regains his sanity (see above for details), he tells Snivley (who's gloating to him from the outside of Eggman's jail cell) that he's figured out why Sonic always beats him. It's not because Sonic is tenacious, or that it's Sonic's destiny as the hero or whatever; it's because he's absorbed so much chaos energy - more than anyone else has - that he's become a living Deus ex Machina able to warp reality to give him Super Luck. ATTN Ian Flynn: Giving a canonical reason for your protagonist to be a God-Mode Sue doesn't make it okay.
There are two possible explanations for this: It's not so much the raw amount of Chaos Energy Sonic absorbed, as it is the length of time in which it was absorbed; a billion rings (which even the Ancient Walkers commented on) and multiple super transformations in a mere ten years in universe (Robotnik's takeover happened when Sonic was five). Or, Eggman's incapable of realizing his own ego's the problem and the Chaos Factor may just be his way of rationalizing Sonic's victories.
Back in the four issue miniseries that started this comic, before Cerebus Syndrome kicked in: In the second issue, Princess Sally goes to the edge of the Great Forest. At Knothole, Sonic and the others find a proclamation from her that she's going to bargin with Robotnik over her father's life. Sonic and others suspect that Robotnik will go back on his word (he does) and go rescue her. They stop Robotnik just before he roboticizes Sally, and take her back to Knothole. Once there, she yells at them for screwing things up. Apparently, she intended for Robotnik to roboticize her because she was wearing devices in her boots that would have analyzed the machine and told them everything they needed to reverse the process. Sally angrily blames them for screwing up the plan. No one points out that Sally could have told them the plan before she did it. In fact, before things go wrong, Sonic asks her what she's doing out on the edge of the forest only for her to yell that it's none of his business. Yeah, Sally, a plan that involves your getting roboticized is definitely not the business of a high-ranking Freedom Fighter... It's lucky she gained some IQ points before the comic proper started.
The entire "Family Matters" arc (Sonic #215-216) is an incredibly divisive arc for many reasons.
First and foremost is the revelation that Rotor retired from the Freedom Fighters after two incidents in the past that left him convinced of his worthlessness as a team member (plus his screwed-up back). One was an on-screen event where he and Uncle Chuck built an army of Metal Sonic Troopers that got hijacked by A.D.A.M. before they could be put to good use. The second was a hither-to unseen incident during Sonic's year in space where Rotor attempted to fill the void in the Freedom Fighters by building himself a mech suit and trying to play hero in it, nearly killing some of the members of the Substitute Freedom Fighters in the process. The first one is understandable, but the second one was the breaking point for many. One of the few things that has been established about Rotor is that he knows he works best as the team's tech guy and has no desire to be an action hero, which was made worse when Tails' tech-guy personality started getting imported from the games. And the big reason this was done in the first place was to explain away an incident back in the #140's where Rotor launched into an anti-gun tirade without provocation (which was clearly just Ken Penders expressing his own views on the matter).
The arc has to deal with Eggman taking control over the Walrus Herd (again) since the effects of the original Neuron Bomb were never taken care of, letting Eggman mindcontrol them again if he wished. Silver is able to break the Walruses out of their sonar-mind-control with a concentrated blast of telepathy. There's just one problem: Silver isn't telepathic, he's mostly telekinetic, and even states mere minutes beforehand that all he can do besides throw stuff around is give someone a headache. The machine is explained to work for even non-psychics and that Silver's minor telepathic abilities could work to short it out. This was just too big a big for some to swallow and called Ass Pull.
Lien-Da, former Kommissar and current Grandmaster of the original Dark Egg Legion, had her head blown up by a bomb put in her by Eggman and detonated by the Iron Queen. Before this, she had betrayed both individuals for her own gain, promting said bomb implant and detonation. Eggman is perfectly aware of this. So, what does he do? Fix her up, puts a new bomb in her, and offers her another chance to work under him. His reasoning? He fully expects anyone under his command to be a Reliable Traitor. Read that; he always expects all of his minions to betray him, sooner or later, but expects them to work for him to their fullest, until then. To paraphrase, Megatron: "Why, that's what they always asked me. Why them? Why Snivley and Lien-Da? Why, out of all of my minions, do I take back the ones whose history of treachery is legend? Because I'm an idiot, that's why!". But that's not the end of it; after being told this, Lien-Da accepts the offer. I don't care if Eggman was in the nut house for twelve issues, or that Lien-Da had part of her brain vaporized, neither of them should be this stupid.
This stupid or this Genre Savvy? If you think about it, anyone competent enough to be a Grandmaster is also going to have the ambition to not settle for being second in command. If Eggman gets rid of Snively and Lein-da, he'll be forced to either settle for incompetent mooks (Scratch and Grounder, anyone?) or train a whole new group of Legionairres that will ultimately turn on him anyway. Better the devil you know.
That could be a good point...had it not been established that Eggman (and the Iron Dominion, which Eggman has since taken control from) had established multiple factions of the Dark Egg Legion elsewhere, not just relying on the Echidnas. Should the Echidnas have gone against him, he could've just wiped them out and replaced them with a faction that he KNOWS would do a better job at following his orders. It's not as if, to our knowledge, any of them have bombs in their cybernetics to keep them in line, like the Echidnas do.
Issue #221. Just...the level of hate and bigotry in it is sickening. In case you're wondering, it deals with two basic themes:
Espio, NICOLE, and Dimitri all sulk about how they "betrayed" their friends and countrymen to the enemy, angsting about how they wouldn't be trusted, in the future. The thing is, none of them actually did any betraying; all three were forced into their position by the bad guys (Espio through his aforementioned connection to the ninja clans loyal to the Iron Dominion, NICOLE through the aforementioned Magitek, and Dimitri through an Enemy Mine situation against Knuxerjak and the backstabbing of Lien-Da), and not only were those stints very short-lived, they actually used their positions to work against the enemy, afterward (NICOLE as a Reverse Mole, Dimitri as a Spanner in the Works, and Espio...by dropping off the face of the arc, altogether. Oh, he did get the MacGuffin that finally defeated the Iron Dominion, though). Like the Rotor example above, Ian is using a Fake Defector storyline they had no control over and actually used to the good guys' advantage as the source of a Conflict Ball Hackey Sack game between them.
Mina Mongoose, scarred for life from the events of the ID arc for the wrong reasons (misblaming NICOLE for terrorizing New Mobotropolis instead of the ID), rallies a mob of her fans against NICOLE with a song created to smear her. It's even hinted that her manager and boyfriend, Ash, had to do some Executive Meddling to tone the lyrics down, implying that her hatred toward the computer has reached Westboro Baptist Church levels. Like much of Ian's other "Character Development", this is totally against Mina's core characterization and was not hinted at one iota until now. Even worse, it's explicitly pointed out to them by Sonic and Sally that it wasn't NICOLE's fault, that she worked against the ID during her "betrayal", and, oh yeah, she helped save their asses before, during, and after the invasion by teleporting them to a safe place, yet neither Mina nor the mob seem to accept that, and continue to berate NICOLE, after the Kirk Summation. Yeah, okay, it's explained away that Ixus Naugus was using his magic as a sort of Hate Plague on them (really, Potto? More Diabolus ex Machina from you?), but that only goes for the audience, not Mina, and it does not excuse the sudden sadistic turn that they give against NICOLE (one of the mob actually asked her point-blank if she would feel pain if he stomped on a patch of flowers in the city, knowing it was made of nanites she controlled. Congrats, Ian, you've just introduced blatant threats of physical violence and unrepentant torture into a Funny Animal comic).
To be fair though, it ties into the previous Wall Banger that the Freedom Fighters had become overly confident about NICOLE and hadn't even bothered to take any precaution against obvious threats to her. When Mina calls them out on this, they act equally irrational and arrogant, not seeing any reason for her complaints and refusing to make any changes to their current status because "NICOLE is a nice person and might be upset by it". They knew horrible things had happened because of their recklessness about her, and still expected them to be okay with them doing nothing to prevent it happening again, so Mina is not really that unfounded in her attitude towards them.
Let's talk about two unliked characters in the comic; Tommy Turtle and Drago Wolf. The former is considered the Creator's Pet by most fans, while the latter is considered The Load and a villain with 0% Approval Rating. The former died twice and was shoehorned into most shots involving the Brain Trust as an attempt to make him more beloved; the latter was beaten within an inch of his life constantly and was shoehorned into most villain group appearances in order to get his ass kicked. The problem? Both had potential to be really good supporting characters, mostly through their connections to other characters (the former with Rotor, the latter with Hershey Cat and the Wolf Pack Freedom Fighters), but the writers were just too damn lazy to do so, resulting in their hated status. Seriously, if we can give Robotnik's niece the same kind of love and respect we give the main characters, then why not these two?
The "Chosen One" saga. Oy, if there were ever headaches about a story in the comics pre-Ian Flynn, this had to be it. Supposedly about a prophecy stated to have Tails destroy then-megaenemy Mammoth Mogul and use the Chaos Emeralds to bring about a "golden age", it wound up becoming a mess of writers having no idea what that was supposed to mean and clashing explanations for what Tails was supposed to do. It gave us the horror of "Titan Tails", spanned all three head writers (Penders, Flynn, and Karl Bollers), and wound up being an utter waste, as even after Flynn put an end to the nonsense, Mogul is still around as a villain and there is still no "Golden Age" for Mobius.
Flynn eventually resolved the whole "Chosen One" debacle by actually doing something that the original prophecy said: by having Tails be a conduit that would send every Chaos Emerald in the universe into the Zone of Silence where Feist would reduced their number (and increase their power) to seven, finally matching the game universe's canonical number. Oh, and the kicker about Titan Tails? He was also drawn horribly bad and overmuscled, so even his appearance couldn't salvage his mess of a storyline. Not to mention Titan Tails was brought to us by the same writer who created (and brought back to everyone's horror) Tommy Turtle.
Here's one about the Brotherhood of Guardians. When Robotnik took over, the Brotherhood naturally lost contact with the Kingdom of Acorn. It's unclear exactly when they learned about Robotnik, but probably before Sonic and Knuckles first met. During the various tie-in issues involving Knuckles, Robotnik had attempted to weaponize Angel Island, indirectly threatened it's destruction, conspired with local criminals to smuggle his tech onto the island, and tried to destroy it outright with the Death Egg. We have no explanation why the Brotherhood never took him out themselves even though doing so would be protecting their home from a major threat and the Knuckles series showing that they had the mystic abilities to just teleport into his control room and banish him into a pocket zone.
This is one of the big problems with the Brotherhood themselves: you know the Watchers? Uatu and them? Yeah, they're supposed to act in that capacity. They have all of this power, but they want the current Guardian to figure all of this shit out him/herself. The only time they step in is if it's something that goes vastly beyond the Guardian's capacity. They only rescued Queen Alicia and Prince Elias because of the Overlander threat that might come about and the only known time prior to Sonic and Knuckles' first encounter that they stepped in for Knuckles was to banish a bully off the island. Everything else? It was on Knuckles' head. Then again, it's been established that many echidnas are natural jerks who tend to think high and mighty of themselves.
Here's a problem with Naugus becoming king: the guy's a convicted criminal. He was serving time for his various crimes, such as the attacks on the Freedom Fighters and Nate Morgan to gain the throne and siding with Mammoth Mogul-time he didn't finish serving. How did the council, that had Rotor and Uncle Chuck on it, not take any of this into consideration since they're the authority? Even if Naugus was given the right to rule by Max, doesn't allying with one of the kingdom's biggest enemies count as treason, making him ineligible to claim the throne? It's like the episode in The Simpsons where Sideshow Bob became mayor because he rigged the election; just because you take the top spot doesn't excuse what you did to get there. Of course, we may never know what would've originally happened when the Naugus arc ended thanks to the reboot.
Naugus used his magic to enhance their fears of Nicole & growing doubt about their King's ability to protect them from the Empire. Given that New Mobotropolis was attacked several times in a very short time and that Naugus, who displayed power to help combat threats to the city and had legitmate right to rule. Not to mention that between getting thrown into the Zone of Silence and getting put into a cell with no real trial while not in a right state of mind, could mean that he was never actually convicted of any of the crimes he had done... or that at least he had time served.
Naugus was mentally sound when he teamed up with Mogul, so that should be able to stand up in trial. There's also the fact that Geoffrey explained that he and Naugus willingly let Robotnik take over the kingdom based solely on the notion that Max wouldn't listen. Not only does that not explain why they couldn't tell someone else, or at least get Naugus released and then he'd stop Robotnik, doesn't it also open Naugus up for treason again since he willingly endangered his nation? Whenever someone does this "cause destruction for the greater good" schtick, it's still viewed as wrong or at least morally ambiguous. Honestly, it seems like Naugus is manipulating the council's collective grudges with the royal family and FF, not helping is that Uncle Chuck's seemed to have lost some nerve to just let this fly to begin with, so well that they aren't realizing any of this.
Geoffry & Naugus didn't let Robotnik take over; they were suspicious of him since he was a power-hungry Overlander, but they didn't have much proof he was about to betray the kingdom (it could be argued that Kodos getting thrown in the Zone could be payback for his role in starting the Great War, even if Robotnik did do it to gain more power). Geoffrey's age (six-or-so at the time) and loss of his father (killed by an Overlander attack) could be seen by Max or a member of the Court as a child raging out due to his loss.
Still doesn't cover Naugus teaming up with Mogul. In fact, didn't Naugus possess Max before and tried to get the then Robian population dismantled? That didn't cause any concerns for the council?
Somewhat, IIRC Naugus just enhanced Max's distrust for Robians after the King had announced he had wanted them dismantled, but he didn't quite brainwash him completely per se. To Naugus, the Robians just represented more of Robotnik's technology and nothing more; so with (nearly) all the Robians returned to normal, he wouldn't go to persecute any of the civilians who would be part of his kingdom. ...Of course, he would, but that's not quite the issue. His first attempt to seize the throne after the return of Max could be seen as him reclaiming his "claim" to it; same with him teaming up with Mogul. The alliance could be seen as the "true King" allying himself to gain the tools of the kingdom. Mogul didn't really do anything against the kingdom aside from antagonizing Sonic & Tails; his attacks on Echinopolis & Knuckles wasn't against the Kingdom Of Acorn himself, so he didn't technically commit treason against the kingdom before he seized the Sword & Crown.
In Mogul's second appearance, he attacked the Freedom Fighters (including Sally) using the Sword of Acorns with the intent to fake his death the further his own plans. He's also told Sonic point blank that he won't try to conquer the world until after Sonic's dead. That's enough to prove Mogul's an actual threat to the Kingdom, and that Naugus committed treason by allying with him. Especially since after Mogul lost the Sword of Acorns, Naugus obtained it, only to give it back to Mogul. Naugus willingly gave aid and comfort to an enemy of his nation.
If Mogul allies himself with the "Rightful King", then he could be made part of the Royal Court right? An "advisor" or something (depending on how long Naugus would remain loyal to Mogul or if Mogul wouldn't mind being The Man Behind the Man). In that case, he wouldn't threaten the Kingdom, since through he and Naugus, it would be the Kingdom that would threaten to conquer the world, with Mogul & Naugus already in charge, so that charge of treason may not apply (I guess; I don't have the best knowlege of the innerworkings of politics, monarchial or otherwise when it comes down to it).
The whole reason the Echidnas, as well as many other supporting characters, have vanished and the reboot even happened: Ken Penders & his copyright claims & lawsuits. Even after Archie & Sega settled with Penders, the man had the gall to say that Archie Comics could still use his characters, but with having consultation rights over them, demanding a licencing fee for their use and making the canon future the massively unpopular "25 Years Later" arc. And after the comics were forced to do a reboot, Ken responded incredibly immaturely.
Making the 25YL arc canon is especially pointless since it's meant to be a prequel to the stories he's planning to write about Lara-Su. Problem is, he can only write those stories if they aren't connected to the Sonic books. It's like he just wants to use the Sonic books to try and rebuild his old plans from when he was head writer.
Which in a way feels eerily similar to the attempted Hostile Show Takeover that happened with Novas Aventuras De Megaman, where one of the writers attempted to have all of the characters killed off or at least completely replaced with his own creation, with little regard to the Capcom characters. Anyone know if there was ever a comic published in Brazil called "The Princess Chronicles"?
Does anyone remember Nate Morgan? For a time during the Bollers era, he was a semi-major supporting character (he introduced Sonic & the Freedom Fighters to Station Square for the Sonic Adventure adaptation). He was given a lot of importance: to the Royal Family with King Max, to Chuck for being one of his teachers and the making of Rings, to being used by Kodos & Naugus to create more distrust to fuel the Great War... ever wonder what happened to him? He was given a very low-key, almost avoidable Heroic Sacrifice by being roboticized into a statue by Robotnik (along with Snively & Hope's father, Colin who also had a role to play in the backstory, for inadvertently introducing Julian to the Mobians). Any hope of rescue was dashed when Robotropolis was nuked by Station Square's WarGames-esque defense program and the roboticized people were nuked to ashes. How long was Nate mourned for after this? ...Three issues at least? And he was almost never mentioned again. Karl Bollers had at least a potential story idea where Nate somehow survived and got manipulated into building the Doll series of Metals, but that was dashed when Bollers left the book. What a way to go, huh?
In retrospect, Robotnik's plan in Endgame should've started falling apart from the beginning. Drago framed Sonic for killing Sally by tricking Hershey into wearing a Sonic costume with rigged eye pieces to make everyone look like Snively. The problems are as follow:
Did Hershey not look into a mirror when she was in the costume, or not look at anyone until she went out to cut Sally's rope?
At that point in the book, Hershey was drawn as being taller than Sonic. How did Antoine, who saw Hershey's murder attempt, not notice that Sonic had somehow gotten much taller than normal?
Endgame was about the third time Sonic was framed for treason and Sally's earlier mini-series, which Geoffrey debuted in, established that Robotnik could build robots that flawlessly imitated real people, so why did everyone buy into this at face value?
Sonic's cleared of all charges because Dulcy, saying that Dragons can sense truth, vouches for him. This is treated as common enough knowledge that it raises the question why she wasn't called in earlier.
Mecha Madness is one of the most cherished episodes in the series, and with good reason, but it does feature a wallbanger of its own: namely the revelation that there's apparently a stockpile of nuclear warheads just lying around in the middle of Robotropolis. This brings up a few problems:
First off, nuclear weapons don't work like that. Unlike conventional explosives, nuclear weapons - by their very nature - need to be properly triggered before they can blow up. Two robots slamming into them at supersonic speed is unlikely to do anything except wreck the weapons in question and possibly lead to radiation contamination of the area.
Then there's the issue that two Mobian-sized robots at ground zero somehow survived an explosion that blew apart buildings and other, human-sized robots of similar make. Never mind that the detonation of multiple nuclear warheads at the same time would generate temperatures where the bots would simply flat-out melt (or, more likely, be completely vaporised), regardless of the pressures and other destructive forces at work. The comic never gets into payload, but it's somewhat surprising that any of Robotropolis survived the blast.
Also keep in mind that Mecha Madness' story started in issue 39, and in issue 37, Robotropolis was heavily damaged by an earthquake. Were the nukes stored there before that, or moved after? If before, why didn't they go off then?
Issue 40, which wraps up the MM's remaining plot points, ends with Sonic using Nack's sky sled as a missile to attack Robotropolis, exploding a nuclear power plant that was just brought back online. As you'd expect at this point, the plant explodes like a nuke, causing a shock wave that's felt all the way back in Knothole. This time however, Robotnik was caught in the blast. How did he, or anything left in Robotropolis after the last three issues, survive?