During the Endgame arc, a Knothole traitor shows just how cruel a double-agent to Robotnik can be by arranging a vicious assassination of Princess Sally Acorn, which also frames Sonic for the deed.
Also during that arc, Snively showing his true colors by reprogramming his uncle's ultimate weapon to backfire on him... and only him, leaving everyone else unharmed for him to torture.
That's to say nothing of Sonic and Robotnik's final battle before all is said and done, with both of them discarding any words or taunts, and just focusing on beating the crap out of one another. What follows is one of the series' most brutal battles, rendered by one of the series' most popular artists, Patrick Spaziante.
The entire Mecha Madness arc. Sonic is finally captured and roboticized by Robotnik and sent to destroy his friends, who clamor to find a way to stop him. Choosing an incredibly risky plan, Bunnie stalls Mecha-Sonic while Knuckles is roboticized with a neural implant to keep his mind free, climaxing in several pages of Mecha-Sonic vs Mecha-Knuckles that ends with both of them caught in (and surviving) a massive explosion.
Made even more awesome with the realization that it was written by Mike Gallagher, who is far more well known for the pun-laden early issues.
Sally slugging her for it, which was agreed upon in-universe:
Sonic: Actually, I thought it was kind of hot!
Monkey Khan: Totally in agreement there!
Tails: Yeah! Next time you should hit her again!
Fiona gets another one afterward by engineering a prison break for Scourge...and kicking him in the groin for his prior douchiness toward her when he was "King".
Dr Eggman gets a true CmoA in #175 by facing Sonic single-handedly in his new Battle Armor, which was powerful enough to resist a full-speed charge from Sonic (which didn't do more then dent his shield). Dr Eggman didn't just beat Sonic, he also deals out a Breaking Speech as he does, before finally leaving him to wallow in his defeat. This, of course, proves to be a big mistake later.
Of course, the events of #175 just make the Sonic and Eggman rematch confrontation in #200 even better.
A rather understated one follows in subsequent issues, when Sonic and team manage to regroup in a new city, and subsequently work together to dismantle the very armor Eggman beat Sonic in, with Sally then telling him that they can take him on at any time or any place once he's fallen at their feet.
In #179, Elias and Tails' father get into a dramatic one-on-one battle over who should be in charge of the Kingdom of Acorn. Sally breaks it up with a Death Glare, tells them both off for their behavior, then asks pointedly if they're ready to discuss the issue like sensible people. By the time Sonic makes the scene, they're compromising over tea.
Mad Scientist (In every sense of the word) echidna Dr Finitevus effortlessly manipulating damn near everyone, turning Knuckles into a super weapon and then calmly letting himself plummet off the island into a warp ring with a smile and a wave.
Enerjak facing off against Eggman's entire fleet. Hundreds of ships, a city full of killer robots, missiles, death rays the whole thing. Enerjak proceeds to destroy EVERY SINGLE ONE. And for good measure he turns Eggman's city into a wasteland, with only one small part of it even being halfway habitable now. All Eggman can do is stammer in agreement to Dimitri's suggestion that it's time to get to his fall out bunker.
Jules gets one in issue #192, where he talks down Scourge, a guy who had previously conquered a whole planet, never flinching despite the repeated threats, and sending the thug away in tears.
Even more amazing is that after Sonic defeats Robotnik and drives him into his Villainous Breakdown, Snively comes along and explains Robotnik's deteriorating mental health. He subtly calls Sonic out for constantly winning over the years despite Robotnik's intellect and resources, the main reason Robotnik snapped. When he asks Sonic to just leave him alone so he can take care of his uncle, Sonic is left in a funk as he realizes what he had done in order to win, his joy turned into emptiness all because on Snively's speech.
Which may be a covert CMoA for Snively, allowing him to set up the Iron Queen's ascent.
E-102 gets some in Sonic Universe #3, overall surviving as long as he did counting as one. Later, Gamma manages to knock Omega on his ass with a few well placed shots, while delivering a speech in his cold monotone. He then lets Omega blow him up after copying his own data into the walking arsenal's mind and fusing with him, effectively giving Omega a true soul.
Silver manages to pull one off when he paralyzes a room full of combatants, including Sonic, Scourge, and Metal Sonic, with his telekinetic powers.
Issue #210. Robotnik managed to reason himself out of insanity.
Bunnie destroying Eggman's battleship.
Issue #204: After spending over 150 issues taking several hundred levels in badass, Antoine vents his anger on Monkey Khan for not telling the Freedom Fighters about the Iron Queen and her powers, which he was powerless against, and which almost got Antoine's wife, Bunnie, killed.
Issue #205: Eggman (while still insane, mind you) manages to escape from his cell, get in one of his giant mechs, and escape from the Iron Dominion, scaring away all the mooks in his resulting rampage, all while dropping Mythology Gags and Continuity Porn.
I am Warlord-Doctor Julian Ivo Eggman Robo-Kintobor Mach Two! My rule is law, and the law is my will! AND I HATE THAT HEDGEHOG!!
Sonic Universe #25 - Enerjak - and by extension Knuckles, given that he is Enerjak! - shows that he can be just as - if not more - menacing than the original Robotnik. When Silver arrives in his world, he at first views Silver, before returning to his prisoner, Constable Remington. As Remington gives a typical heroic speech about Enerjak being stopped, Enerjak holds out his hand and rips out Remington's soul, before the comic pans to a shot of Enerjak holding the latest soul, and revealing every hero and villain in the world is also on his wall, having likewise had their souls taken. This is emphasised by Enerjak saying that nothing can stop him.
References to Enerjak's power are made throughout the arc, including that He sank Mobius' version of Australia, hitting Silver with Angel Island, and his ability to summon all the souls he's taken at once to form a massive army. It is even implied that only Enerjak can defeat Enerjak, something Silver uses to his advantage.
Issue #224, when the Death Egg Mark 2 launches into the air and causes the entire planet to shake.
Sonic Universe #28 - Silver defeats Enerjak. During Enerjak's rant on how superior he is, Silver realizes that Enerjak is correct; he can't match Enerjak's power. As such, he begins to use his ESP powers to instead capture Enerjak's energy and send it back at him, bringing the demigod to his knees with each shot the arrogant overlord throws at him.
Issue #225, the whole thing, for Eggman. Silver Sonic V3 is one by itself.
Even Sonic admits that last bit is awesome.
Dr. Eggman has one when he seemingly actually kills Sally. Ladies and gentlemens, the Man ChildDiminishing Villain Threat-suffering nutcase is now officially gone and the evil Dr. Ivo Robotnik we all once loved to hate has returned to stay.
Made even more awesome by the fact that he's savoring his victory by holding a glass of wine while firing his superweapon.
And even though the original plan was reversed and Sally revived, issue #230 gives Eggman an awesome Consolation Prize - the re-roboticized Princess Sally: Metal Sally!
The Batman Gambit Ixis Naugus carries out from Issues #221 - #224. He casts a spell on the citizens of New Mobotropolis that magnifies their mistrust and fear of NICOLE (following her temporary corruption by the Iron Dominion) into full-blown paranoia and hate. This is so that he can show up and claim to "save" them from the "threat" that the Freedom Fighters have left running around, if they just make him king. And he's only stopped at the last minute by the arrival of the Death Egg presenting a bigger threat.
And then Issue #230 rolled around...
In light of the criticisms in the recent DC reboot and Marvel's less than stellar approach to ending relationships in comics, the current writer deserves some praise for handling both ideas with much better results than the big two comic publishers.note The reboot has been criticized for some rather sexist depictions of women and Marvel's had a tendency to end marriages in stupid ways, such as One More Day. By comparison, the Genesis arc has caused some big changes in the status quo and Sally sacrificed herself to save the planet.
The hits keep coming for Dr. Eggman! In issue 234, Dr. Eggman detonates Metal Sonic, almost murdering Antoine D'Coolette. That's right - in the span of four issues, Eggman has crippled, if not destroyed, the Freedom Fighters.
Issue 235, Silver returns once more and tells Sonic he has determined that Antoine is the traitor he's looking for. Sonic, for reasons that's mentioned in the spoiler above, puts Silver through a wall, then drags him to Antoine's bed and shows him that he is not the traitor he's looking for.
SU 37, Eggman puts all the Grandmasters into their place, reminding them who's boss despite his previous Diminishing Villain Threat.
"I'm winning this war."
SU 40 knocks it up even more: Thanks to Snively's attempt at The Dog Bites Back, G.U.N. is weakened, Eggman knows where his niece Hope is, the hold of the Dark Egg Legion is even tighter than before and he now has the Iron Queen at his side. And he does this as he gloats to a defeated and broken Snively, trapped in his own prison.
Tails gets an awesome moment in issue 238. He's secretly placing a tracking device on the Death Egg, when he's attacked by Metal Sally, who lampshades that Tails' emotional attachments will prevent him from fighting back. Wrong. Tails immediately repels her with a spinning tail attack, uses his momentum to slam her into the ground, and successfully hold her off. He points out to her that he's sorry, but he will protect himself. Had Tails not had other concerns and had to break away, its hinted that he could actually have won.
If you take into account that Sally has essentially raised Tails along with the other Freedom Fighters, its made all the more poignant, because he's fighting off somebody like a mother to him. It's another indicator as to how far he's grown as a character.
Naugus gets one in Universe 43: When he reveals that he plans to use his magic to mentally enslave the council to his will, Geoffrey objects, saying that it goes too far. Naugus than counters that Geoffrey's not one to talk about morality given his past actions. He also reminds Geoffrey that he can't beat him on his own and no Freedom Fighter would trust him; Naugus' way is his only option. Geoffrey, horrified, hands over the item Naugus needs to cast his spell.
And another in 241: With his mutations getting further out of control, being rejected when he tries to form contracts with Max and Jules to possess them to hide said mutations, and the people's fear of Nicole have waned enough that the council will let her back in; basically, he's steadily losing control. Geoffrey still tries to appeal to Naugus better nature and work to atone for their crimes. Naugus however realizes that Geoffrey is still under contract with him, and possesses him. After Nicole's welcomed back, "Geoffrey" informs the council that Naugus is dying and asks to work with him to help the king...
In this same vein, we also see Crowning Moments from Max Acorn, Bernie and Jules AND Isabella, Mina's mother, all three of them essentially giving Naugus one "The Reason You Suck" Speech after another.
Shadow the Hedgehog gets one which proves his straight up badassery when facing Eggman of all people. When he comes on to Eggman's underwater base alongside Bunnie Rabbot and personally scares Eggman with threats of death, Eggman exclaims to Shadow that heroes don't kill while Shadow simply replies, "Sonic may hold such beliefs, but I do not." This is the first time Robotnik has been terrified of a character in the comic.
The Secret Freedom Fighters in general in issue #240, but Shard, the rebuilt original Metal Sonic, takes the cake by shredding through Eggman's new model. "Accept no imitations," indeed.
There's also the team attacking Naugus in his secret underground lair in Universe 44, disrupting the spell he was going to use to brainwash the council and most of the city. The entire fight is awesome.
One for Silver: By staying in the present, Silver has helped stop Naugus's plan to use mind control on the council, enabling Nicole's return to the city. Additionally, Shard saved Antoine from Metal Sonic. As of 247, he saved Team Fighters from being killed by Mecha Sally (who he's confirmed as his target thanks to Harvey explaining her 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. Antoine would be dead. New Mobotropolis might've died by this point, because Naugus wouldn't allow Nicole back into the city, likely would've disbanded Team Freedom, and might not have healed his condition enough to stop the Tails Dolls. 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. But Silver's presence has changed things enough that they'll all survive. To think that he's had this much of an impact is just astounding.
Eggman arguably has one of the biggest Moments of Awesome for a villain ever at the end of the crossover: he messes with Sonic's Chaos Control, causes almost the entirety of the Multiverse to collapse and even Sonic's world is barely hanging on by a thread. To clarify: Eggman managed to SUCCEED at doing what hundreds of Omnicidal Maniacs have dreamed of doing, destroyed almost all of reality, COMPLETELY BY ACCIDENT. Bonus points for doing so just to screw with Sonic. Eat your heart out, Anti-Monitor.
Even more-so when you consider that with only the Sega, SATAM, and Ian Flynn elements still in the book, thanks to the Penders lawsuit, this means Eggman has effectively wiped out nearly all of his villainous competition. By accident.