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There are two people behind the chao disappearances. Eggman Nega is stealing to feed the Ifrit. Eating the Chao alive will make the Ifrit invincible. Silver is stealing the chao to hide them from Nega.
Silver did go home after the first game, only to a ruined future caused by Nega's awakening of the Ifrit. Chaotic Inferno looks very much like Crisis City, and the Ifrit wrecked Silver's world like Iblis did.
After the Ifrit is defeated, Nega is left under the rubble in the Ifrit's dimension.
Also, the Ifrit's boss battle is pretty dang sweet. You're falling in fire and Ifrit attacks you as does Metal Sonic 3.0. Pushing the X or O buttons at the right time makes you do a slow mo hit on the Ifrit. After a few of these it'll stop and try to crush you on it's stomach (which you can walk on). You have to hit his head three times to make him vulnerable, and then a fourth to damage. Eight hits kills it.
Silver's PK is limited....and can be recharged. (like in gameplay) If he overuses it, he gets tired. All of Frontier Canyon is spent collecting Rings to restore Silver's powers.
Silver goes back home at the end of the game, and hopes the new future is a good one. (most likely won't be ya idiot since you left Nega in the past)
Silver and Espio worked together because, though Espio thought Silver's story was ridiculous, he also felt that he should trust him.
Silver has one heck of an attitude as well. He's arrogant, bossy, and heroic at the same time. It's like a combination of Shadow and Sonic with a bit of youthful naivety thrown in. It's like he's a douche because he has to be or something.
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Rouge was hired by Nega to find the Chaos Emeralds.
Rouge flirts...a LOT.
The M.E. was in the Emerald Detector Knux and Rouge stole from Eggman
Knuckles only works with Rouge because he has to, to find the M.E.
Knuckles and Rouge work moderately well together, though Rouge's motives are entirely selfish.
Rouge didn't want to go to the Ifrit's world, but Knuckles practically dragged her there (she tells him to let her go).
Knuckles and Rouge's interaction seemed duty based on Knuckles's part and playful on Rouge's part.
Rouge is currently in possession of the M.E. She tells Knuckles that she thought he was dashing and heroic during the adventure, and thusly steals the Emerald while he goes into modest mode about himself.
Knuckles and Espio are acquainted with one another, and Knuckles is aware of Espio's chameleon like abilities
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In Mystic haunt, Sonic and Tails encounter phantom versions of themselves. The story art for them looks like a possessed Sonic and Tails with red eyes and no legs. All they do is laugh evilly. Sonic and Tails see Eggman Nega with the phantoms and think he's a phantom of Eggman.
The Ifrit possesses Tails (and possessed Knuckles too while I'm at it), and thusly Sonic (and Rouge) have to take out Tails (and Knuckles) AND the Ifrit. The possessed characters attempt to fight it, but it's not enough not to make them a threat.
The client who wanted info about the Chao disappearances in never revealed. Also, he/she paid in advance and Vector spent the money on rent payments for the office.
Espio does learn of Eggman Nega.