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The plot is basicly the same as the original. Dr. Eggman discovers the legend of Chaos, the god of destruction. He releases Chaos from his prison in the Master Emerald and plans on collecting the seven Chaos Emeralds to power him up.
|Image||Name||Bio||Style of gameplay|
|Sonic the Hedgehog||Sonic is the fastest creature on the planet. He is best friends with Tails and spends his days relaxing. But now he finds himself trying to stop Eggman's latest scheme involving Chaos. Can Sonic stop his enemy from destroying Station Square?||Normal (Get to the goal of the stage)|
|Miles "Tails" Prower||Sonic's best buddy and a great inventor. He is responsible for the creation of Sonic's jet plane, the Tornado, and has always followed Sonic wherever he goes. But now, he has to muster up the courage to adventure on his own when Eggman threatens to destroy the city.||Race (Get to the goal before your CPU opponent does.)|
|Knuckles the Echidna||A friendly rival to Sonic and the last of his kind. To this day, he has guarded the Master Emerald on Angel Island. But thanks to Eggman, it has shattered into numerous pieces. Can Knuckles re-assemble the pieces?||Treasure Hunting (Find all three pieces of the Master Emerald in the stage)|
|Amy Rose||Sonic's biggest fan and self-proclaimed girlfriend. For years, she has always been the damsel-in-distress, with Sonic always being forced to save her. But now, she finds herself back in the spotlight when she becomes the bodyguard of a little blue Flicky that is being chased by Eggman's power-house, E-100 Alpha.||Chase (Get to the balloon at the end of the stage before E-100 Alpha catches you)|
|Big the Cat||A lazy fisherman who spends his days fishing with his best friend, Froggy. One day, Froggy swallows a strange puddle and Big's lucky charm and runs off, sending Big on a wild goose chase. Little does Big know, his lucky charm is one of the Chaos Emeralds, and the strange puddle is a piece of Chaos, and Eggman wants them both!||Fishing (Find and fish out Froggy)|
|E-102 Gamma||One of Eggman's newest creations. He is the third of the E-100 Series, and has been built by Eggman to help in his mission to control Chaos. But after seeing what happens when an Eggman robot fails, and with a little help from Amy, Gamma turns on his master and decides to free the animals inside his brothers. Will he succeed?||Shooting (Destroy your target before time runs out)|
Playable in Multiplayer
|Image||Name||Bio||Style of gameplay|
|Metal Sonic||A robot duplicate of Sonic who really wants to eliminate him. Sometimes, he's even gone as far as betraying Eggman.||Long Race (Same as Normal, except now you have to get to the finish before your opponent)|
|Charmy Bee||The youngest member of the Chaotix detective agency. His keen personality may be a little annoying, but his skills are what makes him a member.||Short Race (Same as Race in Single-player)|
|Rouge the Bat||A treasure hunter working for GUN. Her hobby is collecting jewels for herself, and sometimes she targets the Master Emerald.||Treasure Hunting|
|Espio the Chameleon||The serious member of the Chaotix detective agency. He is a skillful ninja, and is considered to be the sneakiest one of the three.||Chase|
|Vector the Crocodile||The leader of the Chaotix detective agency. He enjoys listening to rock music and solving mysteries with Espio and Charmy, on account that he is paid, of course.||Fishing|
|E-123 Omega||Gamma's younger brother and a member of GUN. He has this urge to destroy Eggman's robots for revenge, but has a kind soul just like his brother.||Shooting|
|Dr. Eggman||Sonic's arch-enemy and a crazy mad scientist. After learning about the legend of Chaos, and releasing the monster from his prison, Eggman plans to use this beast to destroy Station Square and replace it with Robotnikland. All he needs are the seven Chaos Emeralds, and he has his robots looking for them!|
|Chaos||The god of destruction. After years of being trapped inside the Master Emerald, he has been released by Dr. Eggman, and is now looking for the Chaos Emeralds with him. Every time he gets another Chaos Emerald, he changes into a stronger form. Can Sonic and friends stop this monster from getting all seven?|
|Tikal the Echidna||A mysterious girl from the past. Throughout the story, Sonic and friends get visions of her in the past. Are these visions trying to tell them something?|
|Pachacamac||Tikal's father from the past. He is responsible for the anger of Chaos and the almost-extincion of the Knuckles blood of echidnas.|
|E-100 Alpha||A tough robot created by Eggman. Nicknamed Zero, he has been tasked with the mission of capturing a Flicky who has swallowed one of the Chaos Emeralds. And Amy's caught in the middle.|
|E-101 Beta||Gamma's older and more advanced brother. After losing to Gamma and being put into storage, he has been remodeled into a Mark II robot, and is more powerful than before. Can Gamma destroy this monstrous robot and free the bird inside of him?|
|Froggy||Big's pet frog and best friend. He has swallowed the tail of Chaos and one of the Chaos Emeralds. Now Big has to go find him before Eggman catches him.|
|Chaos 0||This is the form Chaos takes when he has no Chaos Emeralds. You will face him immediately when you start the game. You will find him threatening the police in Station Square. You must hit him three times to defeat him, just watch out for his extending arms!||Sonic|
|Chaos 2||Eggman has used the two Chaos Emeralds he stole from Sonic and Tails near Tails' Workshop and at Casinopolis to make Chaos stronger!! In this form, Chaos can now turn into a giant ball of water, and use an energy shield.||Knuckles|
|Chaos 4||After duping Knuckles into battling Sonic and Tails, Eggman has swiped the Chaos Emeralds the duo obtained at Windy Valley and Ice Cap, bringing the number of emeralds he has to four, making Chaos turn into a stronger form again!! Now he can fire energy waves and swim at high speeds!!||Sonic, Tails and Knuckles|
|Chaos 6||The final boss of Knuckles and Big's stories. Thanks to the two Chaos Emeralds Eggman obtained from Froggy and Amy's blue flicky, Chaos is almost fully powered up!! Use the nearby ice-generating robots to freeze him up!! And don't forget to fish out Froggy while your at it!||Sonic, Knuckles and Big|
|Egg Hornet||One of Eggman's Egg Mobile modifications. He really wants the Chaos Emerald you have to power up Chaos!! Hit him three times to destroy his ride.||Sonic and Tails|
|Egg Viper||The final boss of Sonic's story. You got Eggman on the ropes! Now he's called in his latest mega-machine to face you, with it's spiked discs, lasers and balls of electricity!! Hit him seven times to finish Eggman off once and for all!!||Sonic|
|Egg Walker||The final boss of Tails' story. Eggman's rampaging through Station Square on this giant mech!! Incapacitate the legs and hit him five times to save the day!!||Tails|
|E-100 Alpha||The final boss of Amy's story. After being chased by Alpha for the course of the story, it's time to destroy him once and for all! Push him into the electric fence and press his self-destruct button multiple times to defeat him!!||Amy|
|E-101 Beta||Eggman wants to see if you have the guts to stay onboard the Egg Carrier, so he has called E-101 Beta to battle you! Blast him three times to defeat him!||E-102 Gamma|
|E-103 Delta||After failing to catch Froggy, E-103 Delta has been relocated to Windy Valley. Blast him and free the animal inside him!!||E-102 Gamma|
|E-104 Epsilon||After failing to catch Froggy, E-104 Epsilon has been relocated to Red Mountain. He's a little harder to destroy than E-103 Delta, so be careful!!||E-102 Gamma|
|E-105 Zeta||After failing to catch Froggy, E-105 Zeta has been re-built into a stronger form deep within the Hot Shelter. Avoid his rocket turrets and blast this improved machine to free the animal inside him!!||E-102 Gamma|
|E-101 Beta MKII||The final boss of E-102 Gamma's story. Since your last battle with E-101 Beta, Eggman has upgraded him into a MKII robot, with more features than his younger brothers! Don't give up though, find his weaknesses and free the white Flicky inside him!!||E-102 Gamma|
|Perfect Chaos||The final boss of the whole game! Tikal tried to warn everybody, but now, filled with rage from 4,000 years ago and the negative power of the emeralds, Chaos has activated the super transformation to become this beast, and has flooded Station Square!!! All hope is not lost though! Use your own super state to neutralize him once and for all!!!||Super Sonic|
In this single-player mode, players will play as one of six characters, each with their own side of the story. At first, only Sonic will be available to play as, when the player meets one of the other playable characters in the HUB world, that character is automaticlly unlocked. Once all six characters' stories are finished, one final story will be unlocked, which fetures Super Sonic against the final boss of the game.
A new mode made for this version of the game. In this mode, two players compete against each other in one of six modes; Long Race, Short Race, Treasure Hunting, Chase, Fishing and Shooting. Each mode features the character that's playable in the other modes, and an exclusive character for the second player. This mode can be played in Download Play or Wi-Fi.
In this mode, players can compete in stages they have already beaten to earn more emblems. They can also compete in mini-games they have unlocked in the game.
In this mode, players go running around the HUB world, collecting missions for you to accept and play.
This mode won't be available at first, it'll be unlocked when players collect twenty emblems. In this mode, players can play classic games from the past. Due to the Game Gear titles from the DX version being downloadable, instead, players can play titles that were previously available on the Sega Genesis. When you collect a certain amount of emblems, a new game will be unlocked.
In this mode, players can unlock various things to look at by clearing certain achievements in the main game and the Mega Collection mode games. Things that you can see in this mode include the covers of Archie Sonic publications up to the present (Sonic Issues 1-255, Knuckles Issues 1-32, Sonic Super Special Issues 1-15, Sonic Universe Issues 1-59, Sonic X Issues 1-40, all Mini-Series issues, all 48-page specials, all reprint issues, all digital reprints, SSS Magazine issues 1-8, Sonic Super Digest Issues 1-3, all Free Comic Book Day specials, crossover issues like Mega Man Issues 24-27 and others), readable versions of Sonic's Firsts, Sonic the Hedgehog Issues 71 to 84, and Sonic Super Special Issue 13, illustrations of Sonic, Tails, Knuckles, Dr. Eggman, other characters and Misc., manuals of Sonic Adventure's many releases and all the Mega Collection games, and a video history of Sonic up to the present.
In this mode, players can interact with their virtual Chao pets. They can bring animals they free from Eggman's robots in the Action stages to the garden, and use them on their Chao to let them gain more stats. There is also a Black Market where players can purchase food for their Chao and new Chao eggs, and a Chao race where player's Chao run through an obstacle corse. New to this version of the game is StreetPass functionallity. A player can choose one of their Chao and put them in the StreetPass Walker (replacing the Mini-Chao Garden teleporter), when a player passes by another player with the game, they exchange data, by tagging eachother, players can compare their Chao stats, pit them in a duel Chao Race, and collect points to unlock more items in the Black Market.
In this mode, players can customize their gaming experience by choosing Stereo or Mono, or which file they want to play. Plus they can listen to sounds and music, change the menu announcer and what language the characters speak in.
Games in Mega Collection
Throughout the HUB worlds, there are hidden upgrade items that add or improve abilities for a certain character.