Since when do people debate over timelines in Sonic (Besides the 3D babies, who only then talk about the 3D games)?
Maybe I'm crazy, maybe there's too much Zelda influence, but Sonic has a plot!
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Plot Arc #1- The Numbered games
Sonic- Robotnik takes over an island, but it defeated by sonic and flees to another island. Sonic follows him, and thus we get...
Sonic 2- Now having followed Robotnik to Island #2, Sonic teams up with tails to stop the creation of the Death Egg, Robotnnik's new doomsday machine. They save the day, but it crashes on Angel Island, home of...
Sonic 3- Again on a different island, Robotnik is rebuilding his Death Egg, and using a native of the island, Knuckles, to delay Sonic. The DE is almost lauched, when Sonic destroys it, sending it careening back into Angel Island.
Sonic and Knuckles- In the meantime, Robotnik has created the Egg-Robo, which he sends after Knuckles for being a pretty useless henchman and holder of more magical jewels. Now that everyone is out to get Robotnik, he's doomed, and the day is saved. Since the Death Egg rubble is out floating in space, Robotnik needs a new plan.
There were a number of spin-offs, but I haven't played them all, so I can't tell the story. I do know the 3-D games, so that means...
Plot Arc #2- Adventure
Adventure- Robotnik has landed back on Earth, and has decided to resurrect an ancient god of chaos. That affects everyone in the Sonic series, and Robotnik is doomed again. Since he's incompetent with giant floating ships, he decides to go use his ancestor's machines in...
Adventure 2- Now Eggman has revived his grandfather's creation, Shadow, and the Space Colony ARK. With those and a gorgeous bat, he trys to take over the world. (Of course!) Again, everyone defeats Eggy, and Shadow jumps out the window, starting...
Plot Arc #3- The Shadow Chronicles
Sonic Heroes- A bunch of stuff happens here, but all that's significant is Shadow. He's survived, and has no memory of anything. After saving the world, Rouge discovers that there are several Shadows, which come into play in...
Shadow the Hedgehog- It's just Shadow backstory. I know that that's no detail, but it has relation to the arc.
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And there you have it. I haven't really played through the Post-Shadow games, so I can't comment. The point is the every Sonic game in the main series has some baring on a series of plot arcs. Each has a different tone, but that can, for the most part, be tied together.