Where is Omega during the Last Story? He's a robot, he would also be immune to the nerve gas. All that firepower could sure come in handy.
Omega is an E-100 series robot, and as a result is still being powered by an animal. The nerve gas might make him power down due to the animal being affected.
Why on EARTH was Dr. Eggman on the Black Comet in Last Story? It would make sense if he showed up piloting the Egg Breaker or in his Eggmobile or even on his floating screen, but he's on foot! He doesn't even have anything to defend himself with, like a squad of Egg Pawns! Must've been clutching that Idiot Ball pretty close, Ivo...
And Sonic and friends, huh? They're strong enough, they could survive easily. Eggman was WITH them, not as a enemy for that situation, of course. Having them as "temporary allies" against Black Doom left him a reason to do that.
The President at one point mentions while looking at a picture of Sonic and Shadow that "The world was once saved by you two heroes". Now, he's probably talking about SA2, or possibly Heroes, but regardless of that... when was the picture taken?!
My take is sometime between Sonic Heroes and Shadow the Hedgehog. Shadow was thought to be dead at the end of SA2, so it couldn't be right after that game.
I'm guessing just after Sonic Heroes; after the incidents of that game, Sonic and Shadow had been responsible for saving the world. Only plot issue is why none of the other teams were in the picture.
Why does it cost "ammo" to put out fire? Also, how does he refill its "ammo"?
He uses a water gun?
The motivation of the Black Arms is that they want to eat us. Keep in mind that they've been waiting for this meal for over 2000 years, so why haven't they starved by now? Even if you argue that they've got really good metabolism or have been hibernating, their comet-home means that they've never been able to try this before.
Maybe their "going hungry" lasts longer than a normal human's?
Still doesn't explain how such a species could evolve if their eating habits require such a complicated gambit. Though it could just be that we're simply more nutritious/tasty than their comet's vegetation.
Who's to say that Earth was the only planet the Black Arms had/were going to invade? The Archie Sonic Comics canon says that the Black Arms have fed on other worlds while waiting for Mobius/Earth to reach a certain population level so the Arms could invade and have a planet wide smorgasbord.
Also, remember that, without the seven Chaos Emeralds, the Black Arms have no way of controlling where the Black Comet goes. The first couple times the Black Comet passed the earth, the Black Arms could have appeared, gotten a taste of humanity, so to speak, but were forced to leave before the Black Comet got too far away. During one of the trips, Black Doom helped Gerald with the Ultimate Life Form Project as a long term plan for the Black Arms. By having an agent to get them the seven Chaos Emeralds, Black Doom could warp the Black Comet to the planet, spread its paralyzing nerve gas all over, and basically have an all-you-can-eat buffet for the Black Arms (and more importantly, the newly born Black Arms), which would allow them to replenish their numbers, then use the Chaos Emeralds to warp the Black Comet back into space, get to another planet, and repeat for infinity.
If Shadow wants to find out whether he's a robot or not, why doesn't he just cut himself to see if he can bleed? Or use an X-ray to determine whether his skeleton is metal or not? Or simply weigh himself?
Shadow never seems to bleed anyway; the intro cutscene sees him shrugging off bullets and explosions, and in game all taking a hit seems to do is knock him down and cost him rings (and far fewer rings than Sonic usually loses, mind). I think it's safe to assume that while he can be killed with sufficient effort, he doesen't really take injuries. As for X-ray machine, he saw the androids, then immediately chased down Eggman, who told him for certain that he was an android, and he believed that. There was no time when he was uncertain in which he could have gone and done anything to test it.
It wouldn't have worked anyway since the idea of an android is a living outer skin over a robotic skeleton and interior.
Ah yes, Shadow cutting himself. As if he hasn't tried that already. Lord knows he's angsty enough.
How is a melee weapon capable of refilling its "ammo"?
By having more than one of the same weapon. When the first one breaks, Shadow starts using the second one, etc. They just don't show the switch because it's easier that way.
If the Black Arms can be harmed and even killed by standard firearms, which GUN possesses, shouldn't GUN be winning by a considerably huge margin?
The initial attack by the Black Arms was effectively a blitzkreig that caught G.U.N. completely off guard. Depending on which one Shadow sides with, they're either able to contain the Black Arms menace, or are pushed all the way back to their Fortress.
But GUN knew Prof. Gerald made contact with Black Doom, which is why they massacred everyone aboard the ARK. Shouldn't they have had records about that to either predict or straight up confirm when the Black Arms would return and plan accordingly? Again, another reason GUN should have been winning by a larger margin than depicted.
If the commander of Gun has such a vendetta against Shadow, how the hell did the military mistake Sonic for Shadow in Sonic Adventure 2? Sure, that plot contrivance was unbelievable as hell to begin with, but this just makes it more absurd.
It's entirely possible that Tower (the G.U.N. Commander's actual name, at least according to the comics) simply wasn't the commander during the events of Sonic Adventure 2, that he was still rising up in the ranks. There's a theory on the Sonic Adventure 2 page that hypothesizes G.U.N. mistaking Sonic for Shadow was intentional. The higher-ups knew from the get-go it was Shadow committing crimes, but they didn't want the public to know about Project SHADOW, so they used Sonic as a scapegoat, manipulating the media accordingly. That pretty much solidifies the possibility that Tower wasn't in command at the time of Sonic Adventure 2. If he was, then he wouldn't have even considered using Sonic as a suspect - he would have just straight up ordered the military police to kill Shadow on the spot.
Rouge is a G.U.N. agent, right? She'd also be on the search for Shadow. I can buy the fact that she just wouldn't report back, taking Sonic Heroes and Sonic Adventure 2 into account, but wouldn't G.U.N. be constantly asking her if she found something?
You probably answered your own question; she probably just wouldn't report back, or would fabricate her reports if they demanded them. GUN already knows that Shadow's out there, they have sentries and soldiers everywhere, but they also know that Shadow is ridiculously skilled at evading arrest and eliminating entire GUN battalions, so Rouge claiming "I didn't see him" or "He escaped from me" doesn't seem out of the realm of possibility to the higher-ups at GUN. As to why she wasn't brought under suspect or a court-martial during the onslaught at GUN Fortress (where there are security cameras and GUN soldiers and mechs in every corridor), either A.) Shadow just evaded the areas with security footage aligning the hallways (which Rouge encourages you to do, probably to evade the cameras herself so they can't use the footage against her afterwards), or B.) GUN was in such a state of disarray and anarchy that nobody was keeping tabs on Rouge at that rate, too preoccupied with tending to the current alien threat, to preoccupied with the safety of the President, the rushed activation of Diablon, and straight-up trying to survive.
Also, two of the Missions where you help Rouge have you either aiding G.U.N. (Death Ruins Hero) or at least working against the Black Arms (G.U.N. Fortress Hero). The second example even has Rouge say that the Chaos Emerald there belongs to G.U.N. and to not let the Black Arms get their claws on it. Even if Rouge did report Shadow showing up in Death Ruins, she just has to point out that he fought on their side there before running off somewhere. We don't know what happens after Shadow beats Black Doom at G.U.N. Fortress and declares he'll conquer the universe. For all we know, he somehow drags G.U.N. into helping him wipe-out the leftover Black Arms and build a new world order (in which case Shadow being a possible enemy wouldn't be an issue anymore).
Why is the G.U.N. Commander... the G.U.N. commander? He was on the ARK when it was attacked and seized by G.U.N., and about the only character motivation he has is that he loved Maria and hates whoever killed her. When he confronts Shadow, it's clear from his dialogue that he blames Shadow for the incident because he's the reason it was attacked. So... instead of blaming the army who infiltrated the ARK and killed everyone, he's blaming the guy they went to the ARK to kill? And not only that, went on and joined up with said army and became their commander? Even if we go at it from the direction of "it's the fault of whoever caused the invasion to be necessary", shouldn't he be blaming Gerald Robotnik and Black Doom, since it was them that created Shadow?
Revenge Before Reason. Honestly, he may not have known. You have to remember, the Commander was a young, young boy at the time of G.U.N.'s raid (read: massacre) aboard the ARK. Too young to fully consider everything, and too angry about losing one of his best friends. He was probably being hauled into an escape pod and hurriedly shot off back down to Earth while Shadow was trying to escape with Maria. After that, he was likely fed some fabricated story that "Shadow was the one who killed Maria" and that nobody else was to blame for the incident. Either that, or he just jumped to conclusions. Kids are prone to mistakes.
Where the heck did Rouge and Knuckles go during the hero endings of G.U.N. Fortress and Black Comet respectively? I mean, Sonic, Vector and Omega were there for their own cutscenes, but why not those two? And for that matter, Black Doom was absent for all the endings he assisted with, and was absent for the Egg Dealer boss fight in Cosmic Fall where Vector was, and Omega hopped out of nowhere for the 'Neutral Dark' boss battle. What gives?
Inconsistency. Or, potentially, because they weren't very relevant to the ending at hand, and were only there for the adjacent boss battle to provide backup and tactical advice. Omega is relevant to the neutral endings because they involved androids, Sonic is relevant to the hero endings because he's there to help eliminate the alien threat, and Vector is relevant cause... uh... he's there? Or maybe the computer room was the place where he and the Chaotix put in all the information and gimmicks they had you collect over the course of the game, like the top-secret prison Island discs or the information from Eggman's cyberspace terminals. Or this is all just a Fan Wank and the game just isn't terribly consistent.
How come the game didn't include a Path/Ending where Shadow joins Eggman to crush their enemies? This gets to the point where you can complete Iron Jungle's Dark Mission and still have the cutscene before its boss where Shadow is running with Omega until Eggman shows up calling the two traitors. Even though Shadow would have aided him in the last Mission.