Following the previous incident, the President had grown fearful of Sonic and his friends, as well as Eggman’s scientific prowess.
He therefore decided to send in an agent (Mr. Stewart) posing as a teacher at Chris’ school.

Just then, reports surface of the discovery of a mysterious stone that could cause machines to malfunction.
Recognizing it as a “Chaos Emerald,” Eggman deployed one of his robots, as well as checked things out himself.
Sonic and his friends also learned about the Chaos Emerald on TV and headed to the scene.
And so, a battle over the Chaos Emerald ensues.