Emerl's death is so completely and totally bizarre as an element of the Sonic series.
Like, as a story element, this does not fit with the rest of the series at all.
Characters don't really die in the Sonic series. There are a handful of villains who snuffed it, but even the bad, unpopular ones linger around like bad smells until a comic writer makes them kill people and a bunch of Youtubers insist that this means they're good characters now.
(If Zavok has no haters I am dead, etc)
But in terms of characters who the audience is meant to be on the side of, death doesn't really happen. The only times it did were Gamma, whose entire story is about reframing the death of the robot as the liberation of the bird inside, and Shadow, whose death was a heroic sacrifice that was undone in the next game. Sage didn't even have to wait that long, with her death being undone in the after-credits of the same game she debuted and died in, and then retconned entirely in DLC.
Meanwhile, Emerl basically gets Old Yeller'd. Like, almost literally. Eggman makes him rabid and Sonic has to take out the shotgun and put down his robot buddy.
I know that technically, Emerl isn't killed by the fight, but by Gerald's self-destruct failsafe, but still. For all intents and purposes, Sonic has to kill Emerl and it's only really an extra twist of the knife that he actually manages to calm him down like he did with Perfect Chaos right before the failsafe kicks in.
And the series has largely responded to this by sweeping Sonic Battle under the rug as much as is physically possible, which was not what they were intending initially. Quite obviously, Sonic Advance 3 is a sequel to it, and it was actually Battle, not the concurrently released Sonic Heroes that was the third game they commissioned Sonic X to adapt. The less said about Sonic X's version of the game's story, the better, but still!
And then after those came out, nothing. For over a decade. Sonic Chronicles: The Dark Brotherhood made reference to Emerl and Sonic Battle, but didn't actually include the character in any way, nor did it include Gemerl, and also it's fairly obvious just from looking at the way Chronicles' story unfolds that it was made with minimal input from SEGA. Archie were barred from using the character in their main books because he was in Sonic X jail, and when they did gain access to him in the Reboot, Battle and Advance 3 were simply added to the history of the new setting. Emerl was already dead, Gemerl is probably just Emerl but painted black, but they barely used him and never explained what his deal was.
Now Gemerl is in IDW, and is explicitly a distinct entity from Emerl, and Emerl finally got acknowledged by official media again through Dark Beginnings, albeit only for a few moments.
Because the thing with Sonic as a franchise, at least the parts that SEGA maintain control over, is that it generally, for the most part, does its level best to keep Eggman's hands clean. He's never shown directly killing people. The collateral damage that his attacks cause is always glossed over. He and Sonic are treated as "friendly enemies" a lot of the time.
Even when IDW introduces two new anti-villains/anti-heroes (what the fuck are Surge and Kit even counted as nowadays?) who hate Eggman for his evil actions and Sonic for not putting a permanent end to him, were not directly harmed by Eggman. Instead, they're kidnapped, modified, and brainwashed into hating both by a rogue Eggman lackey/fanboy, ensuring that Eggman had nothing to do with it in any capacity besides "Disappointed some dude with a crush on him."
Compare that to Fiona in Archie Sonic, who had most of her appearances before SEGA tightened up their control of the book. She was abducted by Robotnik as a child, used for experiments, cloned with the intent of the clone being used as an assassin droid, and left to starve by him when he was done with her. Sonic, for his part, tried to save her, but failed due to inexperience, and then never went back to try again (I do not remember if she was moved to another location, but either way he's never shown to have tried to find her again anyway, nor did he ever tell his side of things). Of course, the comic still didn't actually do anything with this, preferring either ignore it entirely (Penders), vaguely refer to it in past-tense (Bollers), or mention it in the present tense but also make her character revolve entirely around Scourge, neatly sidestepping the issue for Sonic and never bringing it up at all in regards to Eggman (Flynn).
(This is not to say that I think Surge and Kit are worse characters, because that's not true at all. In fact, I think they're much better characters, because at least they actually did something with the trauma instead of using it to make Surge a satellite love interest for another, more annoying character. It's just a point of comparison between a present-day comic where SEGA are steering the boat to a past one where they did not care until much later.)
Eggman might be the main villain of this series, but you're meant to like him. Be entertained by his goofy antics and showmanship. He's the bad guy, but dwelling on the obvious impacts of his many, many crimes would harsh the vibe too much, so they don't do it. And that's probably for the best.
(IDW learned the hard way that you do not pull the pin on the Jason Todd Grenade unless you have a really good answer and also you want to learn what percentage of your fanbase agrees with Jason Todd)
And that all makes it very fucking weird that there was this one time 23 years ago where Eggman just fucking murdered one of the good guys and it not only stuck, but also the character ended up being essentially unpersoned within the series itself for the vast majority of the intervening time.
And the thing is that it isn't even well-handled in the game itself. The characters go out of their way to remove Emerl's dangerous programming from him and render him completely free of his darker side. And then Eggman pops up, shits out a galaxy-destroying cannon, and announces that showing Gizoids more strength than their current link can bring back their programming and factory-reset them.
It's a complete and total ass-pull, and I don't know if the game was trying to be poignant or if it was a case of them going "Oh wait, he's too cool. Better kill him."
And I think this is part of why the "Emerl = Gemerl" theory was so prominent in the intervening years between Advance 3 and IDW. Because if they're the same person, and Gemerl's second lease on life is just Emerl being brought back again, then that overly incongruous death no longer matters. Because Emerl is back! Sure, he came back wrong the first time, but Sonic, Eggman, and Tails got that sorted out. And then they deconfirmed that theory and now we're right back to "Eggman straight-up killed a guy you all like and you're all wilfully ignoring that."
If you treat every game as canon, which is apparently the approach you're supposed to take (except for Chronicles), then Emerl died in pain, and is now both unmourned and forgotten by the rest of the cast, several of whom have relatively positive relationships with the murderer.
Guys maybe you should've just undone the death already. Kinda seems like it might fit better with the tone you want than the way you're doing it now.
