The New World Saga: After Sonic and Friends get Chaos Controlled to the human world Sonic has to hide out with Chris while searching for the whereabouts of his friends while also fighting of Dr. Eggman.
The Chaos Emerald Saga: Sonic and Friends are now more accepted by the public and fight against Eggman to get their hands on the chaos emeralds as they may be the key to getting back home. Eventually Sonic goes super in order to take out Eggman again and ends up scattering the emeralds in the process, this then leads to a second Chaos Control that brings more elements of Sonic's World like Angel Island to the human world.
Chaos Saga: An adaption of the plot of the first Sonic Adventure game. Eggman tries to use Chaos to take over the world and introduces characters like Big and Gamma.
Shadow Saga: An adaption of Sonic Adventure 2's story. Eggman uncovers and awakens Shadow from G.U.N.'s archives using his grandfather's data (It's never explained how Gerald Robotnik existed in the human world while Eggman existed in Sonic's world). Shadow helps Eggman fire the eclipse cannon on the moon but eventually is convinced by Chris to help Sonic protect the world in honor of his fallen friend, Maria Robotnik, eventually leading to his death. The Chaos Control used by Sonic and Shadow in this episode also brings more characters and elements from Sonic's world into the human world.
Egg Moon Saga: A short arc following the events of Eggman blowing up half the moon. The doctor tries to feign remorse for his actions by repairing the moon with a robotic half. This is of course, a plan to manipulate the people of earth against Sonic and once uncovered Dr. Eggman is placed behind bars.
Emerl Saga: A rough adaption of Sonic Battle and Sonic X's take on the Shonen Tournament Arc Trope. Eggman tries to use a copy robot Emerl to break out of prison, after Sonic defeats Emerl he becomes friendly and becomes close to Cream. The president then starts up a battle tournament with a chaos emerald as the prize with many characters from throughout the series entering. Emerl emerges victorious due to his copy ability but the chaos emerald overcharges him and reactivates his old programming causing him to attack. Eventually, Cream and Cheese have to take down their new friend.
Homebound Saga: It's discovered that if Sonic and Friends stay on the human world for too long then both worlds will be caught in a timeline freeze, thus a method back home for everyone is quickly developed and an emotional goodbye is held. Everyone heads back through the portal except for Sonic as Chris shuts the portal down before he can go through unable to accept Sonic leaving. Chris then runs away with Sonic to keep him from leaving but eventually Sonic is able to convince Chris to let him go back.