As far as the eye could see, there was nothing but open ocean. Sonic, Tails, Knuckles and Shadow were all in the X Tornado flying over the ocean looking for the final Chaos Emerald. Tails was using his latest gadget, a Chaos Emerald Locator, to track it down but every few miles it would suddenly say that the emerald was in a completely different direction!
"How long is it going to take to find the last Emerald!? I really need to get back to the Master Emerald, and soon." Knuckles said.
"I don't know, Knuckles." Tails said. Suddenly the X Tornado was hit by a huge gust of wind, and a huge tornado could be seen forming in the distance.
"AH! Were did that come from!?" Sonic yelled from the wing nearly falling off. The tornado was moving quickly toward the X Tornado.
"I don't know! But, it's headed back toward the mainland, and us!" Tails said. Sonic saw something like green lightning flash in the tornado.
"Tails! I think I found out were the last Chaos Emerald is!"
"Were is it, Sonic!?"
"Inside that tornado!" Sonic pointed at the tornado coming at them.
The tornado was soon upon them and Sonic was barely holding on to the X Tornado's wing. Now inside the tornado, Sonic could see a machine at the top of the tornado, most likely 1) what caused the tornado, and 2) were the Chaos Emerald was. Sonic could have sworn he saw some one standing atop the machine holding a staff, before he was pulled off the X Tornado's wing. As he flew toward the machine, he saw the X Tornado ripped to shreds by an unknown force, and his friends, along with the Chaos Emeralds that powered the X Tornado, scattered across the winds of the tornado.
Sonic was in and out of consciousness for the next few days, as he was taken apart and put back together by mysterious men, multiple times. By the third day, he couldn't feel his arms or legs, but there were things in their places, probably mechanical limbs. Sonic never saw any of his friends during his stay, but he did hear of several new "patents".
On the seventh day, he was put into a state of unconsciousness and stayed like that for quite a long time... until he woke up in a small cave without any memories.