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!
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.
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 reallyWASsorry for the carnage he committed. A little too sorry. Vector's "DON'T GO THERE!" comment made it sound like Shadow was going to commitSUICIDE! 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.