It took me a while, but I finally realized that the Karma Meter in Shadow the Hedgehog is a perfect representation of how Chaos Energy works. "Power is enriched by the heart.", "The controller is the one who unifies the chaos." Since he's suffering from amnesia and mind-control, he can't focus his powers as well as he could in SA2, so Shadow's state of mind influences the energy he draws from the Emeralds, and alters his powers, much like in Sonic Adventure, where Sonic and Chaos drew upon completely different "sides" of the Emeralds' powers. When he's full of rage and hatred, he draws on the negative power of the Emeralds and his powers become incredibly violent and destructive, like Chaos was; and when he focuses on rescuing people or destroying evil, he gets the positive energy of the Emeralds, and his powers resemble something closer to Super Sonic: high speed, nigh invincibility, and flight. It just fits so well! — Enlong
Also, why was G.U.N. trying to kill Shadow in SA2? Even if he wasn't the dangerous Prototype that G.U.N. was at the ARK searching for, they tried killing him anyways. But, you think they would know the difference between a giant fucking lizard and a hedgehog, and you would be right! They did! They went after Shadow because of his appearance: A Hedgehog sporting the Black Arms skin color! — Shadowgirl13_chaos
On top of that, when Rouge recovers Professor Robotnik's notes in Sonic Adventure 2, we find out that Biolizard's given name was also Shadow. Assuming G.U.N. knew about this project, and Shadow the Hedgehog was developed in secret, they would've come to one logical conclusion about someone created by the Professor and identifying himself as "Shadow."
Watching some of the Hellfire Commentaries playthroughs of some of the Sonic games, they expressed the view that Shadow being created by the Black Arms (and thus making him a Half-Hedgehog Hybrid) was really stupid and not needed... but at the same time, they puzzled over how Professor Gerald, in his experiments to make the Ultimate Life-Form, went from The Biolizard to Shadow, with no other prototypes in the middle. That's when I realised that him being created by the Black Arms was actually necessary to explain why Gerald made the technological leap that he did: using his own intelligence and resources, the best he could come up with was the Biolizard, a creature which clearly wasn't up to scratch. At that point, he encountered the Black Arms, and they gave him the information and resources he needed to create Shadow — they actually say in the game that "He needed a little help", so they helped him out. The game Shadow the Hedgehog basically explains every plot hole from Sonic Adventure 2, both why the Eclipse cannon was made and how Shadow was made (sorry, Hellfire Comms - no offence was intended).
More detail: The Ultimate Lifeform Project is also fueled by Gerald's desire to treat Maria's NIDS and save her life. This is why the Ultimate Lifeform is intended to have immense regenerative powers. However, the limitations of Gerald's knowledge are made apparent in the weaknesses of the Biolizard prototype, which not only requires a life-support system to sustain it, but is also unstable and inefficent. Note how it stops to catch its breath after every attack cycle, which is why and how Shadow, the completed Ultimate Lifeform, was able to attack its life-support systems. Furthermore, it is unstable, as evidenced by the tumor-like weak spots that begin to sprout over its body in the final battle of Adventure 2. THIS is why Gerald was forced to get biotechnology from the Black Arms, as Maria's time was growing short and he desperately wanted to cure her. Thank goodness he left his original "Stop Black Doom" programming in Shadow when he was driven murderously insane by the GUN attack on the ARK colony that killed Maria.
Why does Egg Dealer have a Shadow Fever option, you may ask? Why, to power up his army of Shadow Androids, of course!
That makes even more sense with those endings - Eggman tells Shadow he's a robot in them.
The last story's Deus ex Machina with the Chaotix seems kinda outta nowhere... until you realize that the three missions you do with them actually help them out because they're all connected. Getting 5 top secret discs from the ruins of... Prison Island, where Shadow and probably a lot of other things from the ARK were being held. Helping Espio getting things from the four different towers... when you realize that they're inside Eggman's systems. Helping Vector find the computer room is also good because... where else are they in the last story? A place with a computer.
How can the ARK's cannon fire in the Last Story, when Shadow was using the Chaos Emeralds to maintain his Super form, when it was stated in Sonic Adventure 2 that the Chaos Emeralds were the power source for the cannon? Because the cannon never fired in SA2, so it's using the remaining power from when Eggman tried to use the Emeralds to fire the cannon at the end of that game.
Apparently, the Sonic universe has a really efficient system for city evacuation. Central City is evacuated in about a day, and Westopolis is evacuated in the time it takes Shadow to run down a hill to it. With all of the evil plots for world domination and other problems throughout the 3D games, of course they'd have efficient evacuation plans!
In the "Android Empire" ending, Omega is going along with Shadow and not showing any reaction to the revelation that he's not "the real Shadow". This is because Omega never met "original Shadow", "android Shadow" is the only Shadow he's ever known.
In Sonic Heroes, Omega saw the room full of androids along with Rouge in the team dark ending. Both of them were already aware of the possibility that this Shadow might be a different one. Rouge chose to ignore it entirely, and Omega simply noted that the original had to exist in some form. Bottom line is, neither of them think it's important any more.
There's a plot hole in SA2 where if Gerald went mad only after everyone else on the station was killed, how could he possibly reconfigure the ARK into a massive cannon on his own, especially with short time left and without a legion of robots? It's answered in this game, as the station was already a giant cannon long before G.U.N.'s interference; all Gerald had to do was change the firing coordinates.
Believe or not, the uses of "damn" and "hell" have meaning in the game. Since the Black Arms serve as a parallel to Hell, there are plenty of tropes in this game that concern the underworld. Two words often used to often describe the underworld: damn and hell.
Shadow'sDarker and Edgier leanings are the most-ridiculed thing about the game—the image of Shadow riding a motorcycle in particular. From that image comes the mechanic of using firearms and hopping into and out of vehicles in real-time...Shadow's pretty much committing Grand Theft Auto, which was, for a time, shorthand for "an adult's game." Couple that with the trend of the Nineties Anti-Hero, which concerned itself with making childhood heroes violent and edgy and more acceptable in mainstream discussion, and you have Shadow the Hedgehog.
The problem is, Sonic and his pals are still very popular with kids. Shadow therefore has to force Grand Theft Auto to comply with Sonic The Hedgehog. Fridge Brilliance kicks in when you realize that the game is deliberately Darker and Edgier to the point of absurdity. Better still, the game knows that it's absurd, but still plays it straight: it has a weapon called the "Omochao Gun" that makes a sound like a toy pop-gun, but it's one of the more powerful weapons in the game.
A lot of people feel that helping the Chaotix is very important in the story thanks to their presence in the Last Story. But there's more than that - the Chaotix is something of a Neutral Party, and that's what Shadow has always tried to be! There are three ways to take the Chaotix path but the most obvious for me is "Wandering's End". Black Doom shows up and tells you to find the Chaos Emeralds. Do that in Westopolis and he complains. Next you end up in Glyphic Canyon (which I feel must be an important location since you can visit it twice). And you encounter Knuckles (Ex-Chaotix member from the old days). You think "Okay, there's an emerald here, I'll get it." He just gets mad AGAIN, so no wonder you turn to the Chaotix! This path neither requires assisting the Blue Blockhead, nor does it require any kind of mass murder on Shadow's part. Flus Shadow gets a flashback!
Other likely paths involve visiting Black Doom's Sky Temple twice, then ending at the Black Comet and fighting Sonic - you're planning on helping Black Doom run the world but he turns out to just want to eat everybody. Or if you fight Eggman, you decide to go your own way. It makes sense because The Last Way takes place on The Comet but Shadow isn't seen teleporting there. It also doesn't require mass genocide - just the destruction of Eggman's robots. You meet Eggman multiple times, so it makes sense that Eggman would tell you that you're the real Shadow in the fight against Devil Doom. You can also help Amy save Cream without affecting the story too much, which explains why she might be so enthusiastic about Shadow! Helping Amy makes sense because when Black Doom teleports you to the temple, Shadow may have become afraid of him.
Several of the endings are completely impossible. The Full Evil ending requires that Shadow decides he, personally wants to see the world destroyed, and not let Black Doom do the job by eating everybody. Another shows Shadow deciding that he doesn't want to rule the world after all. And a third means that Shadow seems to be only willing to serve Black Doom if he's not going to eat people, even though he must surely know by then that he's being used. But actually, Sonic Team is helping you narrow down Shadow's true path.
The Slightly Hero - Dark Ending is full of this. Shadow stays aboard the Ark to protect it, with all of the Chaos Emeralds in his possession. So the only forces defending earth from Black Doom and his army are G.U.N, and Sonic and Pals. And considering what happens during the True final ending, and the fact that Sonic can't go super without the Emeralds... yeah.
Well, Black Doom needed the emeralds to start his endgame in the first place, so it could go either way, really, assuming both sides left Shadow alone.
In Shadow the Hedgehog, human GUN soldiers are knocked down and paralyzed when hit, rather than outright killed, for a couple of obvious reasons; it'd be a little dark for the "E10" rating, not to mention harder to sympathize with Shadow if he was a murderer. But at the game's climax, it's revealed that the Black Arms intended to use humans as an "energy source". Food. And if Shadow completes the Dark Mission for almost any stage, he usually ends up aiding the Black Arms in overrunning the given area; thus, all the soldiers he's rendered helpless and immobile are, in all probability, going to be eaten alive by the conquering aliens.
Slightly Hero — Hero Ending made it sound like Shadow really WAS sorry for the carnage he committed. A little too sorry. Vector's "DON'T GO THERE!" comment made it sound like Shadow was going to commit SUICIDE! And what's worse, it was IMPLIED that he DID! Along with the emeralds... yeah, next time Sonic is down, the world is screwed...
One of the Slightly Hero — Hero paths is even named "Shadow’s Second Death...?"
The video you see in the last story reveals that Professor Gerald was a good person who had genuinely understandable reasons for doing the things he did. However, the video becomes quite horrifying when you realise that it was made before Maria died (as she appears at the end) and therefore, it was made long before the video shown in Sonic Adventure 2. It's just scary to see that he went from a good man to a psychopath who wanted to destroy the earth using the weapons he'd created to SAVE it.