Dr. Robotnik infects Sonic with a deadly Doom virus. Robotnik himself was previously infected and his plan is to trick Sonic into getting the cure and then snatch it away. Sonic meets professor Boobowski, the only man in Mobius who can save him. He tells Sonic that he needs to collect the cure ingredients from different worlds as quickly as possible. Professor Boobowski takes the ingredients from Sonic as he gets them and begins preparing the wonder cure. Robotnik kidnaps the professor just prior to Sonic acquiring the last ingredient. Disguised as Boobowski, Dr. Robotnik tries to trick Sonic into handing over the final ingredient. Sonic recognizes the trap and then the two titans battle it out for a climactic ending fight!
Sonic starts the game with the task of rescuing a damsel in distress. Tiara, a beautiful Manx kitten, has been chained to a wooden platform dangled loosely over a bed of spikes. Without a second thought, Sonic nimbly rescues her from certain doom. Troubled, she thanks him but says that this was a trap set by Sonic's arch enemy Robotnik. She explains that the chains that bound her were laced with a deadly virus, and by touching them, Sonic became infected with the Doom sickness. "Only one man knows the cure, and he's in the castle atop Misty Peak" she continues. Sonic thanks her and dashes off...
Making his way through the woods, Sonic finds himself looking out on a huge sleepy valley prefacing what appears to be the Misty Peak. Stopping only moments to admire the view, Sonic zooms down into the valley to find a route to the castle. Reaching it without much trouble Sonic enters the opened drawbridge with echoes careening off the damp, stone walls. An old, stooped man steps into the courtyard. "Who are you and what do you want?!" yells the man. Sonic, unsure of his predicament exclaims," I'm Sonic and the kitten Tiara told me to find the man in the castle on Misty Peak." The old man, raising an eyebrow, responds, "How do you know Tiara?" Sonic explains how he rescued her ending with, "...and she told me that, I guess, YOU are the only one with the cure?" "That is so. I apologize for being so inhospitable. I'm professor Boobowski and my daughter Tiara was kidnapped by Robotnik a short while ago. Thank you so much for rescuing her-- But enough about that! Let's get you cured!" Boobowski grabs Sonic and they scramble down the basement stairs.
The dangling lamps slowly flicker on with a buzz illuminating an old, classic laboratory, like something from a cheesy sci-fi film. Viles with fluid bubble and boil to life as the professor wakes the old forgotten laboratory. "I haven't been down here in years," exclaims the professor as he leads Sonic down yet another flight of stairs. They enter a large stone room with ancient shields and tapestries hung on its walls resting above floor plates painted with pain-staking detail.
In response to Sonic's questioning glance, Boobowski explains that this is the Twist Chamber. "I'm too old to go and find all of the ingredients for your cure," says Boobowski. "This room lets you get to the different worlds that have what you'll need. This is how it works: Just walk onto the floor plate that represents the world you wish to go to. Tell me you're ready and I'll hit the wall switch to whisk you away."
"How do I get back?" pipes Sonic.
"Well, once you complete the world task you're automatically whisked back. I'll tell you each task and fill you in on pointers to keep you out of trouble."
"Has Robotnik gotten to any of these worlds?" grumbles Sonic.
"Not to my knowledge-- But be careful anyways- Oh! I almost forgot! These worlds are a little different then I'm sure you're used to..."
Sonic squints his eyes wearily, "What do you mean?"
"Well, the gravity in them is a bit strange. You can walk on walls and ceilings and such."
"What?! How can I do that?" barks a wide-eyed Sonic.
"You'll figure it out-- Hurry! You don't have much time! Pick a world and I'll send you there!"