First of all I really don't know if this is the right section for this, if it isn't sorry about posting it here. I'm not sure if this is really what happened or not but apparently there is an game ending glitch that happens during the Metropolis section where you split two parties. When you get to the part of Tails's team and you have to go over to the cannon and defeat a boss, it's supposed to switch back to Sonic's team. But it sometimes doesn't with illegal copies of the game. It did mess up right there for me but I have no idea if it actually was this glitch. Has this happened to anyone else? If it makes a difference I'm using No$gba 2.6a with the No$zoomer. And the game I got was from the rapidshare download of this: 2795 - Sonic Chronicles Dark Brotherhood (U)(Xenophobia)
I hadn't really heard of this before. Make sure you are not missing an event in game that is needed to proceed with the story. Go to www.gamefaqs.com and look up a walkthrough to make sure you hadn't missed anything.
This is after I used a guide. It specifically said: METROPOLIS Switching back to Tails' team, your new objective is to get to the cannon to give Sonic some ground support. It's near where you found the last two Chao eggs. Go back up the escalator and to the tower on the left. Jump down to the ledge, and this time take the right fly point. Now's a good time to save - when you approach the cannon, you'll be attacked by a guardian robot. Once you defeat it, you'll switch back to Sonic's team. And that's when it bugged up. Where I heard this glitch was on Gamefaqs question and answer section.