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.
In Shadow the Hedgehog, 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.
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.