Episode 1: New friendsEdit
- After Sonic and Sally have saved Mobius, a new girl named Amy rose moves into Knothole with Mighty the armadillo and Ray the flying squirel. Amy is determind to be a freedom fighter because she has a crush on Sonic but Sally only lets her help her with small things like food making and caculating. Amy starts to hate Sally for not letting her be around Sonic. Amy eventually gets her way and spends time with Sonic and Tails.
- Mighty becomes very close with Bunnie because they are both strong and like country type things which makes Rotor jealous because Bunnie and Rotor were becoming very close until Mighty came to Knothole. Mighty and Rotor later become friends.
- Ray and Tails become best friends which makes Sonic happy for Tails but feels sad. Ray and Tails later learn they do not have a lot in common as they thought they did.
Episode 2: New enemiesEdit
- Snively begins preparing his revenge on the freedom fighters with his new allies: A bionic Ixis Naugus, A robotisized King Max, Hired bounty hunters: Bean the dynamite, Bark the poloar bear and Fang the sniper and his creation: Metal Sonic.
- Ixis later realizes Snively plans to harm Sonic, Sally and Bunny so Ixis tries to convince Snively not to hurt them but later gets robotisized in the brain which causes total control for Snively. Snively later orders Fang, Bean and Bark to go find freedom fighters to take hostage.
- Sonic, Tails, Ray, Amy and Antione get ambushed during training by Fang, Bean and Bark.
- Sally, Dulcy, Bunnie and Mighy later go and look for Sonic and co. but find a group called Chaotix looking for their friend Charmy who was kidnapped by three fiends (Fang, Bean and Bark) The chaotix join co. and find signs of life in Robotropolis which concerns Sally and later finds her robotisized father only when he attacks her. Mighty destroys him devastating Sally but they move on to find Snively's layer and battle Bean and Bark. Fang and Snively catch Mighty and Bunnie and move them with the rest of the hostages. Sonic gains conciense and Snively makes Sonic battle Metal Sonic, Sonic wins the fight, free's his friends and leaves back to Knothole.
- The Chaotix ask if Mighty would like to join them. Mighty leaves regretfully because he left Amy and Ray but hopes Sonic will care for them.
Episode 3: Knuckles Chaotix part oneEdit
- The Chaotix go looking for Charmy to find that Fang and Metal Sonic have half robotisized him and are taking him to Angel island as bait for a monster on the island.
- The Chaotix go onto the island and meet the "monster" Knuckles the echidna with his best friends Flicky and Cluck. Knuckles has no idea what was in store for him. All Knuckls knew was to guard the Master emerald and protect the islands inhabitants.
- Knuckles joins the Chaotix in hope to stop Fang and Metal Sonic. Knuckles learns that the master emerald has control oer Snively's "badniks" and uses two badniks named Heavy and Bomb to lead them to Charmy.
- Metal Sonic and Fang appear, Knuckles and Mighty fight Metal Sonic while Vector, Espio and the two badniks look for Charmy. Charmy is no where to be found while Metal Sonic absorbs most of the Master emerald's power causing the robot to grow and become red. Metal Sonic kidnappes the emerald and the island falls so Knuckles and the Chaotix go after Metal Sonic as Fang discovers secrets in the island such as an advanced society was once inhabited on the island but was wiped out.
- Side story: Amy's new dolls
- Amy finds three dolls that look like Sonic, Sally and Tails and brings them home and finds they work like voodoo dolls and makes Sonic kiss her.
Episode 4: Knuckles Chaotix part twoEdit
- Knuckles and Mighty pursue Metal Sonic. Vector, Espio and the Badniks find Charmy and Charmy seems to be fine so they return to find that everyone left the island.
- Snively investigates the findings Fang could sample to Snively. Snively realizes the power stones and the power rings have a more stronger connection than Uncle Chuck and the Ancient peoples gave them because there are Emeralds known as the 7 Chaos emeralds that grant limited power but not enough limit to take over a world.
- Knuckles and Mighty defeat the titan Metal Sonic, Restore the Master emerald and return to the island for it is now their home.
- Snively finds one emerald and uses it to make organic badniks and Metal Sonics.
- Side story: Rebuilding the wolf tribe
- Lupe begins to "revive" the wolf tribe by rebuilding the empire outside the caves.
Episode 5: Sonic and Amy/ Le Misreble hoghedgeEdit
- Part 1: Tails is sick and the other freedom fighters are hunting a giant badnik so it's up to Sonic and Amy to find a plant to make tea for Tails.
- Part 2: Antoine tries to pull a prank on Sonic but keeps on getting everyone else hurt.
Episode 6: Snively questEdit
- Snively goes out on a quest to find another chaos emerald so he can creat more deadly badniks. Snively reads a script that describes where to look for chaos emeralds. Snively finds out that it will take more than Badnik's, Buzzbombers and SWATbots to find the emerald as he ventures through the great cave. Snively gets the emerald. Now he has the red emerald and the purple emerald.
- Forshadow: One of the badniks the emeralds produce is Robotnik's corrupted soul and plots to overthrow snively.
Episode 7: Sonic and KnucklesEdit
- Mighty feels bad for leaving Amy and Ray so he them to come. Amy says no because he's not her guardian, she feels old enough to protect herself and wants to stay with Sonic and co. Ray was nowhere to be found.
- They later find out that Ray ran away to find his family because he didn't like anybody. Ray runs into Snively and gets capsuled into a badnik instead of being robotisized.
- Mighty introduces Sonic to Knuckles and the two don't get along. Knuckles think Sonic is a pig and Sonic thinks Knuckles is a jerk. Charmy falls in love with Amy but later finds out shes bratty.
- Meanwhile Snively finds out that the chaos emeralds are not producimg the badniks but using parts from Robotropolis to make the badniks which is dangerous for snively because his layer will be out in the open.
- Robotnik makes a new body for his badnik self to roam in.
Episode 8: Egg-sellent returnEdit
- Robotnik is finished making his body but he needs to figure out how to leave the badniks body. Later while Snively is asleep, Robotnik tries to figure out how to use the chaos emeralds to insert his spirit into the body he created.
- Knuckles and the Chaotix return to Knothole and Knuckles attacks Sonic because he found out some of his ancient (important) scrolls are missing and thinks Sonic took them. Knuckles finds out they did not take them and he explains what happend at angel island so the freedom fighters and chaotix go after Snively.
- Robotnik changes half way into his new body until Snively awakes and uses chaos control to stop the import.
- Snively battles Robotnik by releasing the Badniks, SWATbots and Buzz bombers but the SWATbots take Robotnik's side so Snively releases hoards of Metal Sonics, Metal Sallys and Metal Knuckles'.
- The freedom fighters and chaotix find Snively's layer only to be attacked by Fang, Bean and Bark. They defeat Fang, Bean and Bark and go on only to be caught in a battle between SWATbots and Badniks. Knuckles gets some of the scrolls, then later finds out half of them are missing.
- Sonic read on of the scrolls behind Knuckles's back and learns about the chaos emeralds and the freedom fighters make finding the Emeralds their main priority.
Episode 9: Freedom at stake
- After finding out about Robotnik's revival, the Freedom fighters venture off to warn all the other freedom fighters.
- Snively leaves Robotropolis with the emeralds to rebuild his own empire. Fang, Bean and Bark decide to go their own ways and Fang goes to look for his own chaos emerald.
- Bean and Bark go to look for freedom fighters to join up with.
- Ari returns and battles two metal Sally's.
- Sonic finds out that Sally and Griff have been going out.
- Amy uses N.I.C.O.L.E. to phone her friends from the great cavern to come help them defeat Robotnik again.
Episode 10: Pinecones and AcornsEdit
- Sally gets enraged at Amy for inviting the freedom fighters of the great cavern to come live with them. Sally learns their leader is a bully who used to bully Her and Sonic in kindergarden: Princess Pinecone.
- Amy realizes her voodoo dolls of Tails, Sally and Sonic are robots made by Snively and tries to warm everyone. The next day the dolls multiply into other residents of Knothole and Amy goes mad with power, but snaps out of it and burns the dolls.
- The dolls return and Pinecone and her freedom fighters battle the Tails dolls' to make up to Sally and Sonic.
- Rotor and Dr. Flicky find one Tails doll and find out Snively did not make them, Ixis naugus did under Snively's control. Sonic and Sally plan to go and save Naugus.
Episode 11: Tiara BoobowskiEdit
- Tails and Amy meet a girl named Tiara who is looking for a friend so Tails and Amy think she means a play mate but she is looking for Mighty so Tails and Amy play with her then she explains she needs to find Mighty so they leave for angel island without notice.
- Sonic and Sally find out that Snively left robotropolis with one building standing and Sally see's her dad's robot parts and takes them with her, later she traces Snively's tracks and ends up in the great swamp. Sonic and Sally encounter a Metal Sonic and Metal Sally and defeat them. Sonic finds Naugus and Sally finds more scrolls. Snively seems to be gone. Sally finds Snively is out to harm Tails Amy and Tiara.
- Sonic and Sally get Dulcy and head after the 3. Snively capsules Tiara and Amy and paralyzes Tails then takes them away.
Episode 12: Family FeudEdit
- Snively begins to robotisize Amy and Tiara when Tails comes running and destroys a part of the robotisizer. Tiara and Amy run when Snively grabs Tiara. Amy pulls out another mysterious hammer and attacks Snively. Sonic, Sally and Dulcy make it in time to help Tails, Amy and Tiara. Sonic spin dashes the robotisizer and it is history. The six run out as Snively sends hords of Badniks after them. SWATbots begin attack the badniks as Robotnik ambushes Snively and steals the Red Chaos emerald.
Episode 13: A Mighty storyEdit
- Tiara goes to meet Mighty after Sonic and Sally give her directions to Angel island. Tiara and Mighty meet and talk for hours on end. Tiara explains to The Chaotix how they know eachother.
Episode 1: He will always be thereEdit
- Tails and Amy stumble upon the green emerald and take it to Sonic and Sally. Sonic and Sally start a search for the chaos emeralds.