This may have been addressed in the PS3/360 version, but This Troper only played the Wii version, so he's not sure. Here's the question: did Professor Pickle know that Chip was Light Gaia? There's no way there couldn't have been at least a mention of that in the Gaia Manuscripts unless he was working with a seriously abridged version of them, but then why didn't he say anything when Sonic visited him time and again with Chip by his side? I mean, sure, he Never Asked, but if I knew that the hero I'm depending on was traveling with Dark Gaia's god-in-mortal-form natural counterpart without knowing it, I think I'd at least comment on it.
I personally got the impression that Chip was not Light Gaia's usual form (this is a Headscratchers page, it's okay to leave out spoiler tags), just a weird avatar he was forced into when Eggman prematurely broke the planet apart and woke the Gaias up. Light Gaia obviously must have been in the Gaia Manuscripts, but he probably didn't show up as the little furry fairy Sonic calls Chip.
(Original poster) That theory sounds plausible at face value, but unfortunately it doesn't match the details. The "little furry fairy" is indeed Chip's true form. For proof, remember when Chip was sucked into that mural in the Adabat Temple of Gaia, right before he recovered his memory? The mural in question depicted Light Gaia facing off against Dark Gaia, and the former was in the same form we see him in. Don't ask how I know that considering I haven't played the game in weeks.
The manuscripts might have mentioned him but never really went into detail about what he looked like.
Here's a mind-bender for you. In the opening sequence of the game, Sonic is shown running along Eggman's space fleet with no protection from the vacuum of space. Not only does he survive at least four minutes, but the energy he still has is enough to destroy every piece of defense between him and Eggman. Then, when he reaches the inner sanctuary of the Egg Satellite where he gets transformed into the Werehog, Eggman opens up a window and sucks Sonic into space toward the planet. How exactly did space choose to become tangible after the Werehog shows up?
It didn't. The air pressure was lower outside than inside, but that doesn't mean there wasn't any outside. Of course, the series has adhered to Batman Can Breathe in Space ever since Sonic 2...
There was air in the room and he was blown out.
And then the momentum continued to carry him toward Earth, until gravity kicked in.
But when Super Sonic bursted in through the floor, wouldn't all the air be sucked out BEFORE Eggman opened the window!?
There was a big tunnel of sealing doors before Sonic got to the area where he lost the emeralds. Sure, Sonic broke most of them, but when you're building an air-tight spaceship you build backup sealing doors.
The tunnel of sealing doors and the room where Eggman trapped Super Sonic were on different spaceships entirely.
Sonic's shoes change. His gloves do not. He then gets new gloves every time he switches back. Why one and not the other? Sure, the gloves shred themselves to show claws. Why not have clawed feet too?
Maybe he has clawed feet but his shoes are tougher than his gloves? They do have to withstand a lot of friction.
So the Gaia Temples restore the crust of the Earth to how it was before Eggman blew it up, right? Then why didn't Angel Island return to the Mystic Ruins during this game? It wasn't always floating.
The Master Emerald's still on it and pulling it up.
Why did Sonic leave the Chaos Emeralds in the shrines after they'd been restored? It can't be that the Emeralds needed to stay to be recharged, since the emerald in the Eggmanland temple was there for all of five minutes before Light Gaia formed the Gaia Colossus.
They had to stay in the temples to heal the planet.
How does Light Gaia manage to defeat Dark Gaia without Sonic? He can only hold him for about a minute in the first fight, and in the second he dies after maybe two minutes of fighting. Does he find a super hero every time he wakes up?
It was implied that Chip is very strong in normal situations, but because Eggman woke him up prematurely, he was weaker. Also, he only defeated Dark Gaia once it destroyed the planet, so we can assume Dark was usually weak when they finally fought.
Why does it take a single hit from Sonic to destroy a robot, but multiple combos to do the same with the Werehog?
Sonic's hitting the robot at the speed of sound with his Spin Attack, while his Werehog form's hitting the 'bot at regular (human) speed. Notice how whenever Sonic home-attacks the Egg Fighters/Egg Launchers/etc., he literally sends them flying, usually into a wall or water?
It's worth noting that Sonic can defeat those same robots with a slide kick at even the slowest of speeds or by stomping on them. Make of that what you will.
This troper's theory is that since these new robots are powered by Dark Gaia's energies (Eggman states 'harnessing the power of Dark Gaia' several times; also, you absorb Dark Gaia energy from the robots when you destroy them), they become stronger and tougher at night, similar to what happens to Sonic when he goes werehog.
This troper's theory is that objects moving at or faster than the speed of a bullet impact a target harder than punching it.
WHO THE HELL BUILDS A THEME PARK OVER A LAVA PIT AND A BOTTOMLESS PIT?!
The same person who put deadly rotating spike balls in Twinkle Park?
Eggmanland is a park whose theme is pure, unadulterated malice. Lava and bottomless pits fit the theme quite nicely.
How come that nobody found anything weird or curious about the fact that Chip is a fairy chihuahua thing?
Because nobody finds anything weird of curious about the fact that Sonic is a giant anthropomorphic blue hedgehog. They're just used to see that kind of stuff.
Was Eggman's base in the desert wasteland supposed to have be Eggmanland in construction?
How did Sonic reach Eggman's spaceship in the beginning? Did he fly there as Super Sonic and then power down? If he did, why?
He likely flew into our space as Super Sonic and then powered down. Why? Well, remember! Sonic can only remain in his super form for a limited amount of time, because eventually he will run out of rings to keep him empowered; if he runs out of those rings, then he abruptly changes back to his normal form and falls out of the stratosphere. So odds are he just powered down before that could happen, and then waited for the Emeralds to recharge during his fight with Eggman's spatial fleet. Or, he just waited to whip out the emeralds during a compromising moment like being caught in the palm of a gigantic mech.
What do the numbers the checkpoints give mean? They clearly measure how fast Sonic's going when he passes them but "spd" isn't a recognised unit of speed as far as I can tell. A lot of people seem to assume they're mph, but then boosting through them would have to give a minimum of around 765 which often isn't the case. My guess is it's closer to m/s. Or is there no real world equivalent?
Lost in Translation? Or, it could be a peculiar measurement of speed and distance that's unique to the Sonic universe.
Where on earth were Shadow, Rouge, and GUN? Don't you think that the commander would've noticed there was a little hole in the earth... or was Rouge busy trying to find jewels at the time like she usually is?
Perhaps Sonic Team decided a simpler story, as well as humor, was what was needed to counterwhat happened last time, and that G.U.N., Shadow, and Rouge contributed to making it more confusing and angsty?
Someone on a forum had the theory that Shadow was ill, since he relies on Chaos energy to sustain himself but all the Chaos Emeralds had been drained (that could have caused a significant energy flux). And with Shadow out of action, it would be hard for Rouge to keep up with Sonic on her own when he's running around all over the place. She'd have no way of tracking him even if she used her old SA2 tracker because the Emeralds wouldn't be giving any signal. And GUN aren't likely to be aware of any of the Gaia manuscripts so they wouldn't be able to predict where Sonic's going as well. It could also explain why Knuckles is nowhere - being the Guardian, he'd be aware that the Emeralds had been drained, and that could only make him more paranoid about the Master Emerald. He would still be on Angel Island, guarding it.