Bunnie is the source of a lot of this. For starters, it's kind of coincidental that a rabbit who only becomes partially robotic as soon as the events of the comic start would have the last name "Rabbot" her whole life. It turns out that it's actually supposed to be pronounced "Rah-boh," but people just assumed it was "Rah-bot," her being a (half) robotic rabbit and all, and she just went along with it. (For a similar name pronunciation scenario, but in reverse, see Stephen Colbert.) In addition, the idea that a woman who's robotic from the waist down could conceive and give birth to children is pretty ridiculous, as is the fact that despite her cybernetics being acquired and not genetic traits, her children also are cyborgs. And yet these two facts actually could suffice to explain away each other, since apparently her reproductive structures are functioning, but only can create cyborgs. Still, poor, poor Antoine.
In-Universe: Eggman realized that the reason he could never beat Sonic was that he absorbed so much Chaos Energy, from the billion plus rings he's collected and the various transformations, that he's become an embodiment of chaos, and was always able to thwart his plans.
In the former Archie continuity, Eggman's true name is Julian Kintobor. Julian is the name for John Lennon's son, who was one of the main writers of the song "I am the Walrus," containing the line "I am the eggman." Clever Theme Naming is clever.
In issue 252, the first post-crossover issue, Sonic finds himself in a brand new timeline. Going by how Genesis waves work, Mobius should've gone back to where it was in 247. The reason it didn't return is that, thanks to Eggman trying to stop Sonic's Chaos Control, Sonic was forced to prioritize saving his loved ones and just having a home to go back to over restoring the world and inadvertently imposed an idealized version of Mobius on his reality. This makes things very good for Sonic and his friends: as it's been revealed that the Robotnik who caused a lot of trouble in the early days was Classic Robotnik note the Robotnik from Sonic the Hedgehog to Sonic R), Mobius never had to actively suffer like it did. Even more, all of Eggman's victories, though he remembers them, never happened. This is a happier Mobius. Eggman may have the Eggman Empire, but he'll never have the same success he did with the old Mobius!
Another possibility is that Eggman's actions were because of Silver's time-traveling. In the original timeline that Silver was trying to fix, Naugus had taken over New Mobotropolis with his magic, getting GUNS' two Chaos Emeralds, possibly conquering GUN as well; Naugus may have challenged Eggman before the crossover, a stark contrast to Eggman having the advantage like he actually did. And Eggman preserves his memories when he uses the Genesis Wave, so in the original timeline, Eggman let Sonic restore Mobius because he knew he what was waiting. (Kinda). But because of Silver, Eggman gained a huge advantage, and he would not risk Sonic undoing that.
Looking at the pages for Too Dumb to Live or What An Idiot, you realize that Robotnik/Eggman should've been stopped long ago. But when it was established that Sonic was destined to be the greatest hero of time and space, it becomes clear that the world set things up so that Sonic and Robotnik would inevitably fight to facilitate the former's destiny. The Source Of All manipulated Max to ensure Robotnik's rise to power, Merlin Prower stayed out of the way so as to not interfere, and anyone else (Mammoth Mogul, the Brotherhood of Guardians, Albion, etc.) was simply too full of themselves to otherwise care.
Antoine used to be a Butt-Monkey coward. Then during Sonic's year in space, Patch (at the time just Anti-Ant) switched their lives and pretended to be Antoine to rise in the ranks of the Mobian Military, also dumping Bunnie. After Antoine returned and defeated Anti-Ant, he was portrayed as a lot tougher (although still cautious). Why? Because he'd spent a year in Evil Mobius, hanging with people who will twist your head off at a moment's notice, pretending to be Patch! It's an elasticated version of toughening up in prison.
I noticed something. In Sonic Unleashed, Orbot's original version (SA-55, who he is confirmed to be in Archie) was constantly snarking at Eggman for his hasty actions in freeing Dark Gaia. In Archie, between Orbot and Cubot, who constantly insults Eggman for messing up Sonic's chaos control and causing Unleashed to happen? Orbot, not Cubbot. A clever little nod to the events of the original game.
In the early days, some of Sonic's travels into alternate dimensions were, according to Zonic, to train him for some future destiny that would make him the greatest hero of time and space. In one of these dimensions, Sonic killed the native version of his father-this "training" is supposed to make him to be able to kill his family to save the day. What the hell is Sonic supposed to fight and, more importantly do, that would require him to have that kind of experience?
In the story where Sonic learns of this destiny, the versions of Sally, Amy, and Knuckles are parodies of Sailor Moon, Chibi Moon, and Tuxedo Mask. Depending on how closely they adhere to Sailor Moon canon, Amy is Sally's daughter. Problem is that Amy's a hedgehog, which means that Sally and Knuckles didn't have children. What happened to the alternate Knuckles?
In his spin-off book, it was revealed that Knuckles was bullied by Monk, a much larger gorilla. The Brotherhood of Guardians intervened by tossing Monk off the island. The Floating island. While the BoG's attempt to murder a child has offended some readers, since even killing Monk could've been done more humanely, the horror comes in when you realize that Monk probably wasn't the only bully the BoG had to deal with. They may have already murdered several children prior. Suddenly Thrash feels way more justified in his actions.
Much earlier in the book, Knuckles talked to his mother Lara-Le about why their family broke up. During the talk, Lara brings up her discussion with her mother-in-law, Jenna-Lu, about her frustration with Locke not letting have a role in Knuckles' upbringing. When Lara asks Jenna how she felt when Locke was being trained, Jenna looked up abruptly looked up, smiled, and said that she'd be lost without her husband. The implications are terrifying.
Here's another one for Knuckles: in his spin-off book, it was revealed that he inherited genetic augments from his father, gaining enhanced physical and mental abilities. Yet, despite his enhanced intellect, he blew about four chances to defeat Eggman himself in rather stupid ways. One of these chances involved him gaining the ability to time travel and other godlike powers without going insane. Given that Mobious: 25 Years Later revealed that Locke died of cancer because his genetic enhancements reacted badly with Chaos radiation, could Knuckles have gotten some form of brain damage that explains his actions?
Than again, every inmate is fitted with an inhibitor collar that suppresses powers and even normal physical abilities. It's possible that the collars also suppress certain... feelings as well. Which is fortunate given that one of the prisoners is an alternate universe version of Amy Rose, who's twelve.
Didn't even think of that. Brr.
Oh, and in case you were wondering...no, Scourge being a minor did not stop King Maxx from committing attempted murder. It's strongly implied that the poor bastard was not the first one Maxx has had his goons bludgeon to a pulp, because trying to kill a listless, solitary sixteen-year-old over flimsy pretenses wasn't horrible enough.
Hey, for that matter, how old are Al and Cal? They look like...whatever and they act like young children half the time (always look on the bright side of life).
Sally was roboticized and weaponized. While the first one is bad enough, Eggman started the second one by taking a blowtorch to her and removing components. While she was running on an internal battery originally, her weaponized form lacks this, running mainly on a power ring. Eggman has basically mutilated her and taken out some of her internal organs. For all we know, the battery he removed may have been her heart.
By staying in the present, Silver has helped stop Naugus's plan to use mind control on the council, enabling Nicole to return to the city. As of 247, he saved Team Fighters from being killed by Mecha Sally (who he's confirmed as his target thanks to Harvey Who explaining Sally's roboticization) while Team Freedom fights to stop the Tails Doll from flooding New Mobotropolis with radioactive waste. Now remember that, in the first line of events, Silver wasn't around. New Mobotropolis would've died by this point, because Naugus wouldn't allow Nicole back into the city and likely would've disbanded Team Freedom. Nicole would've died, all alone in Freedom HQ, when the big disaster hit. Team Fighters would've been killed by Sally, a sister figure to Tails and Amy, and Sonic's girlfriend. And then, somehow, the world would've gone to ruin. Let's also remember that Geoffrey kicked all this off by stealing the purple Chaos Emerald for Naugus. In the original timeline, he basically kicked off the apocalypse. And now that the scope of the damage from the reboot's been established Geoffrey helped in bringing about multi-versal death and destruction.
In fact, based on biblical verses, when you look at Naugus's actions and interactions since his restoration to just before the reboot, it's not hard to compare Naugus to the Antichrist. Alternatively, Geoffrey's the Antichrist, who is described as a false prophet in service to "the beast", especially since he views Sonic, who for lack of a better term is the book's metaphor for Christ, as a rival who's in the wrong on how to run the kingdom. Man, the Venture Bros doesn't take its failure theme this far.
And just to compound this, when you look at Knuckles' section in the characters page, and how he botched about four chances to stop Eggman himself, you realize that he played an arguably larger role than Geoffrey did.
Nicole comes from the same alternate timeline as the current version of Eggman. This means that every single one of her friends before being sent back in time is dead, and the one responsible is still screwing things up in the current timeline. And she's completely unaware of it.
Actually no, it isn't. It's kinda iffy, but it's implied that in the original universe, NICOLE came from Penders' "Mobius: X Years Later" timeline, which is now explicitly not canon due Ken wanting to use it as a connection to his pet project with Lara-Su. And even if it wasn't part of M:XYL, that story was still written by Penders, so that otherwise unrelated future can no longer be referenced as such. Odds are, NICOLE has a different origin now...
And Nicole does indeed have a new origin following the reboot. However, while the book can't delve into alternate universes due to threat of litigation, there's no reason to assume that the alternate timeline she came from originally wasn't altered.
In the post-crossover continuity after the failed Genesis Wave, Sonic and Tails have to use NICOLE to restore the memories of the other Freedom Fighters. Doing so, however, has proven to be a traumatic experience as this version of the characters live through memories they may not have experienced first-hand. Thus far, the worst has been Antoine in issue 254, who last we'd seen him, was near-death in a coma. He also remembers that he used to be a coward.
How many worlds did Eggman destroy?
It could be worse than this. The Mega Man characters don't remember what happened, meaning that some of the Super Genesis Wave after-effects affected the Mega Man multiverse. This could mean that the Wave may have wiped out some of the Mega Man universes. Out-universe, Capcom has officially cancelled the Mega Man series. In-universe, is this a consequence of what Eggman and Wily did?
Muttski has been turned into a full Mobian following the reboot. Could some of the off-limits characters have been -de-evolved into regular animals?
Going from the above Fridge Brilliance about Sonic imposing an idealized version of his reality, could the off-limits characters have been unknowingly purged by Sonic himself?
Naugus says that he has legal right to the kingdom because Max gave it to him to survive the Zone of Silence. The problem there is that Max was captured by Robotnik, who then threw him into the Zone. Max was a POW by the time he met Naugus, meaning he had no authority to hand the crown over, so no, Naugus doesn't have any rights to the kingdom. Also, Geoffrey admitted in open court that Naugus ordered him to let Robotnik make his coup. That means that Max wasn't as responsible for Robotnik as everyone thinks, because he deliberately passed up a chance to stop him. For all we know, Naugus may have still been a citizen of the kingdom, making his actions treason.
According to Ian's post in this thread Naugus possessed Max as part of the contract the two made before. Since Max was king at this time, so was Naugus; their contract was fulfilled. Once Sonic expunged Naugus and Max reclaimed his artifacts, Naugus no longer had any rights to the crown. Though it does say a lot about Naugus's magic influence on the people.