At the end of the battle for the Chaos Emeralds with Dr. Robotnik, Sonic crosses time and space and ends up in the human world. He rushes through the highway and is met with the high-speed patrol group S-Team who try to stop him, but he easily outruns them. After the chase, Sonic ends up running through the highway's blockade and falls into a mansion's pool, which he can't swim out from. He is then rescued by a boy named Chris Thorndyke, who lives in the mansion due to his parents being busy with their jobs as a technology business CEO and movie star.

While watching TV at Chris' house, Sonic learns that his friends Cream and Cheese are captured in a high security, top secret military research facility named Route 99. Chris speaks to his grandfather Chuck, and finds out the location of the facility. Sonic successfully sneaks in there, but the rescue operation immediately gets a lot more hectic and dangerous. It is then where Tails arrives at the scene and joins the group.

Dr. Robotnik begins wreaking havoc in the city, taking his E-series robot E-23 Missile Wrist along with him. He then proclaims through a broadcast signal intrusion that he is going to make this world his. Tails and Chris go up against him, but are driven into a corner. That's where Knuckles and Amy make an appearance and join the fight. However, Amy ends up being captured in the struggle. Everybody pins their hopes on Sonic to solve the situation.

From the previous incident, the President becomes aware of Sonic's existence and views Robotnik's scientific power as a threat. Afterwards, an agent (Mr. Stewart) is sent into Chris' school to pose as a teacher. It is then reported that a mysterious stone that causes a machine to malfunction has been discovered. Robotnik and Sonic's group arrive at the scene and get in a struggle, knowing that the stone is a (green) Chaos Emerald. Soon after, Chris obtains the Chaos Emerald, but ends up falling from a high place, with Sonic rescuing him in the nick of time.

Having parted with Sonic and the others, Knuckles, the red-quilled echidna, who is taking independent action, hides in the city. There, he comes in contact with Robotnik, who claims that he wants to collect the Chaos Emeralds to return to their own world and apologizes for the evil deeds he has done until now, asking Knuckles to deal with Sonic. Knuckles is tricked by those words. It is then reported that an unidentified gem has been discovered. It turns out to be a trap Robotnik had made up, but Knuckles and Sonic's group fall for it. That's where Sonic and Knuckles begin their fight. After Knuckles realizes that Robotnik lied to him about wanting to live in peace, he teams up with Sonic to defeat him.

Chris and his classmates go outside the school for an extracurricular lesson. Eggman believes that it is necessary to educate children in order to conquer the world, and sends a robot named E-51 Intelligente to Chris and the others. The robot is highly enthusiastic about teaching, but goes berserk and puts Chris and the others in danger. That's where Sonic rushes in and begins a heroic battle with the robot.

Chris, learning of his school's teacher Mr. Stewart's (who is actually a spy sent by the President) sudden calls to his home, is in a huge panic as he can't let anybody know about Sonic, Tails, Amy, Cream, or Cheese. Of course, they are not known to anyone other than Chuck yet, so the two try their best to hide the secret from Ella and Tanaka. However, Cream and Cheese end up leaving the room without permission and cause an uproar.

Knowing that he is being monitored by the military, Dr. Eggman uses a new robot (E-90) that ends up swallowing the man-made satellites. Because of this, the surface is in mayhem, with Cream ending up unable to watch the TV program she was enjoying. Sonic goes on to try and solve the issue, but the bi-plane Tornado cannot reach the void of space. That's where Tails and Chuck remodel the Tornado, take Sonic on board, and head on to take down Eggman's robot.

Since Chris is going to attend the opening ceremony of a resort establishment, everyone goes to the villa of Chris' house. However, Sonic decides to run off somewhere else. Amy gazes at the sea, wishing to have come here with Sonic. Then, Dr. Eggman arrives at the ceremony's site and wreaks havoc with his robots intent on building his own amusement park in its place. Sonic, aided by Amy, arrives to save the day and Eggman is defeated by Amy, but ends up falling into the ocean, with Sonic going in to save her despite his aquaphobia.

A (cyan) Chaos Emerald is discovered in a stadium that is set to be demolished. Sonic and the others come running for it without a moment's delay, but of course, Eggman arrives there as well and takes the emerald for himself, staring the group down. It is then when Chuck proposes a fair and square baseball match, with Eggman and Sonic's team commencing a competition for the Chaos Emerald.

Due to Chaos Control that happened in episode 1, Rouge the Bat is warped into this world as well, where she continues to be a jewel thief. Soon after, in order to defeat Dr. Robotnik, the office of the President sets up a plan to get Sonic and his friends on their side. Then, they attempt to capture Sonic by making up a hoax about a Chaos Emerald making an appearance. Rouge ends up falling into that trap. The government tells Rouge to become the President's agent, and to infiltrate Dr. Robotnik's base. Rouge, however, finds a (cyan) Chaos Emerald inside the base and fights against a Badnik while trying to rob it.

The Office of the President is polishing up a plan of attack on Eggman's base. The presidential envoys visit Chris' house and ask for Sonic's help, but their negotiations fail. The government attempts to infiltrate Eggman's base with a special force led by Rouge in the gap they escaped the base from previously. Meanwhile, the battle revolving around the (yellow) Chaos Emerald ensues between Eggman, Tails, and Chris' group. Having learned this, Sonic heads out to Chris' group's assistance.

Sonic comes running to help Chris' group from their predicament, but the Chaos Emerald ends up being robbed by Eggman. When Sonic and the others follow him to his base, a battle between Eggman and the government's military unfolds before them there. Rouge, Knuckles, and the others who infiltrated the base set up a bomb in the power sector and attempt to escape, but they are locked up by the shutter door. Sonic has to take it upon himself to obtain the (cyan and yellow) Chaos Emeralds and defeat Eggman.

Eggman's base is destroyed. However, the press conference's topic is focused on Sonic, who is not present. The presidential aide is upset by this, believing that if this goes on, the President will lose his next election. Wanting to somehow raise the President's popularity, he decides to open up Sonic's victory celebration and have the photo of Sonic shaking hands with the President taken by the media. He immediately sends Sonic a written invitation. Chuck prepares brand new tuxedos for Sonic and the others. However, Sonic says he has something else to do. It turns out he promised to meet with Helen, a girl who is Chris' classmate and wheelchair bound. Wanting to have Sonic present at any cost, the aide uses special forces to chase after him.

After his base got destroyed, Dr. Eggman spreads terror through the city with the mobile fortress Egg Fort that was hidden underground. Sonic rushes in to help, but he can't reach the high-flying Egg Fort. Chris and the others, exasperated at the fact that they could have reached it with the X-Tornado, are met with the plane arriving to where they are, brought by Tanaka in a trailer. Sonic boards the X-Tornado and assaults the Egg Fort. The great battle with the Egg Fort starts to unfold.

While above the overseas resort spot, the (green) Chaos Emerald starts reacting, with the fourth (blue) Chaos Emerald appearing to be under the sea. However, Sonic can't swim. That's when the group goes to the diving shop, wears the necessary equipment, and dives into the ocean. The group goes on a search while relying on the Chaos Emerald's signal, and discovers a sunken ship from the age of exploration. When they find the Chaos Emerald there, they are suddenly attacked by Eggman's robot and get in a dire situation.

In Oriental City, Knuckles searches for and reunites with a treasure hunter known as Hawk. The two get out of the dungeon, ride the pedicab, and go to the (red) Chaos Emerald's hiding place. That is where they're met with the pedicab driver from earlier, who turns out to be a female ninja robot (kunoichi) Eggman sent in. Knuckles begins his heroic battle revolving around the Chaos Emerald against the female ninja robot.

Tails and Chris meet the two men who are building a dam right in the middle of the savanna, and question the pointlessness of its construction. They ask for the construction to be stopped, but the men ignore them. After that, Tails and Chris start a protest march in the city while accompanied by the animals. The men oppose them in order to carry out the construction by all possible means. Then, Eggman's robot arrives, finds Sonic and a fight ensues, with the men getting caught up in the mayhem as well.

Chris and the others arrive at the old castle by the lake shore to watch the making of Chris' mother Lindsay's movie. However, the filming is temporarily stopped due to strange noises that occur during the shooting. It turns out that someone ended up moving the hourglass that sealed the ghosts living in the old castle. Because of that, various mysterious phenomena start happening there.

Chris and friends are enjoying a trip on the luxurious passenger boat to the fullest, but Sonic, who runs at supersonic speeds, gets exasperated and anxious at the ship's sluggish pace. When his stress reaches its peak, he resorts to unthinkable actions in an attempt to get home.

The leader of S-Team (Sam) suddenly arrives at Chris' house and challenges Sonic to a race showdown. It appears to be a race carried out at the presidential aide's suggestion in order to elevate the President's popularity. Sonic reluctantly participates and the race showdown begins.

On a summer vacation, Chris takes Tails' group and his school friends along to enjoy summer camp in a certain island country. Then suddenly, a giant Eggman mech that's trying to capture Chris' group descends and crumbles a mountain which floods a river, leading to quite a dire situation.

Chris' dad purchases a ring (actually a Chaos Emerald) in a jewelry store intending for it to be a gift to Chris' mom for their wedding anniversary. On that day, while she is filming in the studio, he calls Chris, Chuck, the leader of S-Team etc. there and secretly plans a flashy surprise party, but having noticed the (purple) Chaos Emerald, Eggman, as well as Rouge and Topaz, surge in as well and cause mayhem.

While fighting Eggman, Sonic suddenly starts going wild. Chuck and Tails' group commence a Sonic capture operation in order to stop him as he's running all around. Knuckles, Amy, and Sam Speed join in as well and their plans get increasingly more complicated.

Knuckles arrives at Chris' house, intending to persuade Sonic into working with Eggman in order to obtain the seventh Chaos Emerald as soon as possible. However, instead of meeting Sonic, Chris ends up listening to what Knuckles has to say, and the two head into the forest where Eggman is.

Chris, wanting to get Sonic and his friends back to their own world as soon as possible, ends up handing the Chaos Emeralds stored by Chuck over to Eggman. Having noticed that, Sonic and the others run after him in a hurry. However, Eggman ends up finding the last (white) Chaos Emerald. A tense battle ensues.