When Eggman tries to use E-23 to take over the world Amy, Knuckles and Tails launch an unsuccessful counterattack, until Sonic arrives, and with a ring from Tails, destroys E-23 and saves Amy with the help of Knuckles.
Chris' teacher is replaced with Mr. Stewart, the President's spy, and the first Chaos Emerald appears at a construction site, it's then a race to the emerald between Eggman and Sonic and friends, with Chris stealing it from Eggman's mobile, and Sonic rescuing him from a nasty drop.
After Eggman tricks Knuckles into blaming Sonic for being stuck in the human world, Knuckles challenges Sonic to a duel allowing Eggman to capture Chris, Amy and Tails using E-47, but Knuckles realizes he's being duped and teams up with Sonic to destroy the robot and save the others.
Eggman tries to use his robot, Intelligente, to brainwash Chris' class but when Intelligente winds up teaching more than brainwashing, Eggman steps in to put the children in permanent detention until a worried Sonic arrives, destroys the robot and saves the class.
When Mr. Stewart drops by for a surprise visit, Chris and Chuck are able to keep Sonic and Friends' stay a secret but after the S-Team Leader, Chris' uncle, arrives things get messier and everyone including Ella and Mr. Tanaka find out Chris' secret.
After Eggman discovers that he is being watched by the military he sends E-90 to swallow the satellite, but this disrupts all television so Chuck and Tails turn Tornado into Tornado X allowing Sonic to enter space and destroy E-90.
After Chris, Amy, Cream and Cheese arrive at a resort, Eggman appears and tries to take over but Sonic arrives and tries to stop him only to be saved by Amy from E-39.
It's Team Sonic vs Team Eggman in a baseball game for a Chaos Emerald, Team Sonic falls behind at first but then wins with a Sonic super-play, only to have Eggman steal the Emerald in the end.
The President plants a fake emerald to try and attract Sonic but Rouge takes the bait instead and winds up searching Eggman's base, with Topaz, for a Chaos Emerald, until she encounters E-70 and has to make an escape.
Tails and Chris discover the third Chaos Emerald in a field and fly for it in the X-Tornado but Eggman and E-51 catch up and trap them, meanwhile Rouge and Topaz launch an attack on Eggman's base.
Sonic saves Tails and Chris from E-51 while Eggman makes off with the Chaos Emerald, at Eggman's base Knuckles appears and helps Rouge plant explosives but they end up trapped. Sonic arrives and is attacked by Eggman and E-18 but Eggman drops the emerald and Sonic grabs it and destroys the robots and Eggman's base.
Sonic decides to take his new friend Helen to pick flowers instead of attending the President's party. The President's aide responds by sending a military unit to capture Sonic.
Rising from the rubble of his former base, Dr. Eggman reveals his new battleship, the Egg Fort, and attacks Station Square. Sonic faces off his nemesis once again on the X-Tornado.
The President demands the search for Dr. Eggman after Sonic destroys the Egg Fort. Meanwhile Sonic and his friends are taking a well-deserved vacation where they discover that another Chaos Emerald is nearby.
After Hawk shows Knuckles the fifth Chaos Emerald, Eggman's E-91 kidnaps Hawk for ransom, but during the trade Rouge enters and Chaos Emerald keep away ensues until Knuckles defeats the robot.
When Sonic, Tails, Chris and the Egg Fort crash land on the Nature Continent after a fight, Tails and Chris protest against a dam while Sonic is caught in a battle against Decoe, Bocoe, E-65 and Eggman.
Chris' mother Lindsey is shooting a movie in a castle and Sonic and his friends are there too. They begin to notice that something is amiss as ghostly figures begin to appear.
Sam Speed challenges Sonic to a race on his new racing car. After much plodding Sonic accepts the challenge but Eggman decides to interrupt the whole thing with his newly invented robot Sumo-Man.
Sonic and his friends are at a camp site where they discover a Chao colony. Meanwhile, Dr. Eggman is also hiking nearby and decides to launch an attack when he encounters Sonic.
Chris' father Nelson purchases a ring made from a Chaos Emerald for his wife Lindsey. Being made aware of its presence, Dr. Eggman attempts to snatch the emerald away from them.
After an encounter with Dr. Eggman, Sonic finds himself unable to stop running. Chris and his grandfather Chuck soon discover that Eggman's E-88 is behind Sonic's problem.
Chris finds himself depressed at the prospect of his friends returning to their home world despite knowing that that is what's best for them. Knuckles meanwhile attempts to orchestrate a truce between Sonic and Eggman so that they may all return home.
Eggman takes Chris hostage after tricking Knuckles and Chris into giving him all six Chaos Emerald. Eggman and Sonic face off once more as Sonic seeks to save Chris and prevent Eggman from obtaining the final emerald.
When Big the Cat and Froggy discover a Chaos Emerald, a strange blue liquid takes over Froggy's body and runs away with the Chaos Emerald. Meanwhile, Lindsey offers Cream with another Chaos Emerald that she had obtained from a jeweler.
Knuckles recalls how Chaos destroyed the Master Emerald. Suspecting that Chaos is controlling Froggy, the gang decide to head their own ways in search of rescuing Froggy and recovering the Chaos Emerald.
Sonic, Tails and Knuckles battles Dr. Eggman on Egg Carrier to save Amy and for the last piece of Master Emerald. Meanwhile Chris and Big are still in search of Froggy.
As Tails is given a hero's welcome after saving Station Square from Eggman's missile attack, Gamma decides to deprogram the mission given to him by Dr. Eggman and assigns himself a new one: to find his E-series brothers and to rescue their animals.
Dr. Eggman reveals to Sonic that he had been double-crossed by Chaos. As Knuckles warns Sonic of dangers of Chaos if he was to obtain the last Chaos Emerald, they are transported to the past by a mysterious red orb.
Sonic and Shadow face off while the rest of the crew seek Dr. Eggman who is now in posession of seven Chaos Emeralds. As the battle unfolds, Knuckles take on Rouge for the control of Master Emerald.
To complete his final revenge, Dr. Robotnik's revenge was to crash ARK into earth, destroying everything and everyone. Sonic must now convince Shadow to help save the world from destruction.
Sonic's world and its creatures called Flickies begin to appear in Chris' world. As the President and his staff discuss how to keep them isolated; Chris worries about what they might do with Sonic.
Sonic and friends readies to ring in the new year on the Thorndyke yacht. As the first sun begins to rise, Egg Moon appears to block the year's first sunrise.
As the President sends in GUN forces to stop Sonic from destroying the Mirror Towers, Dr. Eggman reveals that his Sunshine Balls are secretly brainwashing the citizens to turn against Sonic.
When Sonic stands Amy up on a date she decides to go out with Sam Speed instead. Meanwhile Bokkun reactivates a robot named Emerl to free Eggman from jail.
As Nelson tries to maintain the faltering Thorndyke Industries due to his employees joining the Freedom Movement to emulate Sonic's carefree lifestyle, kitchen appliances begin to cause havoc around town.
Eggman is on the loose and everyone is searching for him. While Mr. Stewart investigates Eggman's whereabouts he is captured along with Chris in Eggman's secret hideout in the sewers.
President hosts a tournament with red Chaos Emerald as the prize to lure Dr. Eggman. It's a heated battle that finds Sonic fighting alongside everyone, even the President himself, but strangely Dr. Eggman has yet to show...
The battle for the red Chaos Emerald is heating up. As contestants duke it out for the glory and the prize it's Emerl who wins the tournament. But when Emerl receives the emerald, its power forces him to go on a rampage and attack everyone in the stadium.
