The moral philosophy within the IDW Comic Sonic series has been sketchy for the past couple of years. I also have the concern that the stories and character arcs of the comics have been going all over the place. So I think I might have a solution for that: SONIC CIVIL WAR! That way, we can focus on all the characters at once, all consulting on one issue. Plus, it can be a way to make progress on some unresolved issues in the series.
Sonic the Hedgehog
Miles "Tails" Prower
Amy Rose
Knuckles the Echidna
Tangle the Lemur
Whisper the Wolf
Jewel the Beetle
Silver the Hedgehog
Blaze the Cat
Jet the Hawk
Wave the Swallow
Storm the Albatross
VS
Shadow the Hedgehog
Surge the Tenrec
Rouge the Bat
E-123 Omega
Vector the Crocodile
Espio the Chameleon
Charmy Bee
Lanolin the Sheep
Belle the Tinker
Kitsunami the Fennec
Rough the Skunk
Tumble the Skunk
Everything started going wrong when Sonic refused to locked "Mr. Tinker" up, and letting Metal Sonic loose. So far, I don't think everyone knows about the latter. In fact, everybody believes Dr. Eggman came back solely because of Dr. Starline. As I recall, most of Starline's attempts were failing. It took the mere sight of a beaten-up Metal Sonic the snap Eggman back to his old self. From that the events followed: the Metal Virus, Surge and Kit's creation, the Clean Sweepstakes. Most people think Sonic has no right to make such decisions and would be fed up with him trying to justify them. I think it's time for everyone the challenge Sonic's moral principals once and for all.
Naturally, once Shadow learns about Sonic setting Metal free, he would turn on him, and of course, Rouge and Omega would follow. Surge, Kitsunami, Rouge and Tumble would also side with him, because it's against Sonic. If Kit's mayhem hasn't been discovered, he could be replace with Clutch. It's because of Sonic and Eggman that he is where he is now anyway. Despite being on Sonic side, the Chaotix are still questioning Sonic chooses lately, especially about the Phantom Rider and the Metal Virus. Lanolin used to look up to Sonic, but I think she could still be on edge for the results his actions have made, since he keeps letting the monsters who attacked her hometown go. I always thought Surge and Belle would form some kind of connection, and Belle would turn against Sonic if she learn about his decision to let Metal go.
At least Sonic would keep a few friends in his corner; Tails, Amy, Knuckles, Silver, Blaze, Tangle, Whisper, and Jewel. The Babylon Rogue would want to help Sonic because Jet wants to keep their rivalry alive until it can be settled once and for all.