The Emerald Within

Summary-
Dr. Ivo Robotnik, fromally known as Dr. Eggman, is dead. It's time to be happy, but also prepare for the worst. There's no telling what else might come to attack this peaceful land. It is 20 years after, and the balance on Mobius is thrown off... Balance. Some one has to be responsible,but who?
After a surprising encounter with their new opponent, something unbelievable is believed to have happened. Their new foe, later revealed as Robotnik the Squirrel, has somehow managed to place the Master emerald inside of the beloved hero, Sonic. A certain someone is not too happy about this, but what can be done about it?
Also... Some other questions to throw out. Why is Shadow suddenly being so nice to Sonic, all of a sudden? Tails never wants him to leave his side? Amy's now after... Shadow? Knuckles is... Angry about the situation, of course... But acting about like Shadow is around Sonic, but somewhat worse, when he is with Shadow?