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Archie's Sonic Comic
The Archie Sonic comic book series has always followed a different (and much more complex) storyline than the games. The cartoon that Archie was instructed to follow was Adventures of Sonic the Hedgehog. Fans didn't like this and requested them to change it. But there was, however, an alternative. There was a Saturday morning cartoon, Sonic The Hedgehog in which Sonic battled Dr. Robotnik with the help of the Freedom Fighters who included Princess Sally, Bunnie Rabbot, Antione D'Coolette, Rotor The Walrus, and Miles "Tails" Prower. But the problem was that this cartoon didn't follow the games as much as Adventures did. Due to fan requests, Archie went to SEGA and requested that a change be made to the content of the book. Sally and the rest of the FF's were already in the book so it wouldn't be hard ushering to gradually add more characters, so around Issue #19, Night of a Thousand Sonics which introduced the popular concept of parallel worlds to the book, fans began to see the storyline go in a different direction.
It hasn't been long since SEGA of America officially considered the Archie comics canon and Archie has recently incorporated the stories of released games into their comics - like the new character designs of Sonic Adventure and other game elements - as well as being allowed to go off on its own. To further prove this, SEGA even allowed Archie to change Dr. Robotnik's look to Eggman (which is a huge turning point in the book at #75). And in order to blot out the problem that Sonic Underground causes due to continuity, SEGA even allowed Archie to make it an alternate universe so that the continuity that already exists will remain in tact. The comic has gone through alot, but it has come a long way.
Another factor is that of the fourth part of End Game, written by Ken Penders who was the premier Sonic writer at the time. The original intention behind Endgame was for it to hold the TRUE death of Princess Sally (one of the main characters and Sonic's current love interest. Sally was supposed to die falling off a building on a reconaissance mission into Robotropolis. She was supposed to have been shot down after running from the building and was supposed to be unknowingly replaced by a Robotnik clone. The clone would have lasted for about ten or so issues and later on, the only one who would discover this would be Tails. Sonic wouldn't have believed him at first until it was too late, only realizing that in his supposed death, also to happen in #50, Dr. Robotnik would have gotten the last laugh after all. Sonic would have become more protective of Tails and would be the assumed leader of the Freedom Fighters.
That development never happened though. SEGA of America stepped in at the last moment saying that they wanted Sally to stay alive for their own reasons. Needless to say, these reasons have yet to be known. At any rate, many of the issues from #50 to about #64 had already been planned on the planned events of #50. Due to Sega's last minute interference, the 48 page #50 was cut to 32 pages at the last second with no way to correct the errors. Even #51 hints at the problems of a "traitor" in Knothole (the robotic Sally) but since Sally was still alive, the entire schematics of the stories had to be changed. Ken Penders and editor Justin Gabrie were forced to cut back the story that fans had been expecting since the beginning and instead of the planned story, we got the first part of the shaky Mobius World Tour lotline - the one that split the Freedom Fighters, as well as Sonic fans down the middle, not to mention Archie's full artist and writing staff.
It seemed like the post Endgame months, especially the months closer to #50, were the worst months with the exceptions of a few. However, things have gotten back on track when the stories began to pick up again around #68 and #69. With Sonic Adventure coming into view, and Sega having new people to not make such bad decisions again, Sega is taking a larger role int hte comics and are working with Archie instead of against them. The comic is finally taking a new direction. All in all, things are fastly rising on the uptake for Sonic. And it's a good thing we got SSS#6 - the Sonic #50 remake which ultimately printed the full final #50 story. Archie did it as a sort of "formal apology" to their fans - something they didn't have to do. It at least shows that sometimes, comic book companies actually listen. Endgame was a case of a company that barged in and made a wrong decision, and a comic company that couldn't give the readers what they wanted. The damage was done, but we're past that now and are finally on the move.