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Sonic: Chaos in Equestria (also known as Sonic the Hedgehog: Chaos in Equestria or abbreviated as Sonic: CIE) is a fanfiction written by Snicket324. It is a crossover of Sonic the Hedgehog and My Little Pony: Friendship is Magic. The story has a darker theme than usual Sonic or MLP fare, which starts with what appears to be a brutal final confrontation between Sonic and Dr. Eggman, which results in the deaths of Sonic's friends, the corruption of the Chaos Emeralds, and the rebirth of Super Sonic as the evil version from Fleetway Comics. In the chaos, Eggman unwittingly transports Sonic to Equestria, where he encounters the Mane Six and befriends them, although there exsists the looming threat of Super Sonic, amongst other familiar faces.
The story has received positive reception and has been well-received by fans. Much of the artwork are commissions by other deviants. The story has a sequel (or rather, second act) called Sonic: Battle for Equestria.
The story starts with Sonic the Hedgehog and his friends, Miles "Tails" Prower, Knuckles the Echidna and Amy Rose boarding the Egg Carrier. There they confront their nemesis, Dr. Ivo Robotnik, otherwise Dr. Eggman. Eggman reveals he has the seven Chaos Emeralds, and captures all except Sonic in capsules. Also revealing Cream the Rabbit, Rouge the Bat and Shadow the Hedgehog in his captivity, Eggman reveals that because of their exposure to the Chaos Emeralds, all of Sonic's friends have latent Chaos energy within them, which he intends to extract from them for an undetermined scheme.
Against Sonic's protests, Eggman proceeds with the extraction process. It apparently proves fatal, appearing to kill all of Sonic's friends. Sonic looks on in abject horror, and goes into rage and despair, going on a rampage across the ship to get revenge on Eggman, wrecking it. Sonic ends up wounded in his side, but reaches the deck, only for Eggman to separate the front section of the ship and take off, but Sonic clings to the hull. As the Egg Carrier retreats back to base, Sonic finally confronts Eggman, having deduced Eggman's plan was to transform the Chaos Emeralds once again into Super Emeralds. However, the attempt failed, having amplified the negative energy of the Chaos Emeralds, corrupting them. Eggman attempts to attack Sonic with laser turrets, missing. He then mocks Sonic over the loss of his friends, to which Sonic, in cold rage, responds by violently breaking his left arm and right leg, crippling him. Despite his injuries, Eggman continues to provoke Sonic into violence. Finally breaking down, the now corrupted Chaos Emeralds transform Sonic into a crazed, destructive version of Super Sonic (based on the evil Super Sonic from Fleetway's Sonic the Comic). Eggman realizes he went too far, and attempts to escape in his Egg Mobile. Super Sonic pursues, sadistically intent on killing him. Eggman unsuccessfully begs for his life, to which Super Sonic ignores. In one final desperate move, Eggman activates a weapon known as the Lethargy Laser (a wormhole-generating cannon). It opens up a portal, pulling the crazed Super Sonic into it, leaving Eggman's fate unknown.
The portal transports Super Sonic to Equestria, sending him careening into a chicken hut. Having heard the crash, Twilight Sparkle and the Mane Six rush to Fluttershy's cottage, where they encounter Super Sonic. Upon noticing them, Super Sonic attacks the Mane Six. Twilight attempts to subdue Super Sonic with a spell, but unintentionally absorbs some of Sonic's memories, showcasing his heroics and true nature. Because of this, Super Sonic depowers back into Sonic. The Mane Six, especially Applejack, begrudgingly take Sonic into Fluttershy's house to recuperate and interrogate him. Upon waking up, Twilight and Applejack aggressively question him, to which Sonic, while confused, responds with his normal, joking demenor, having managed to suppress the trauma of his final confrontation with Eggman. He is confused as to where he is, but he acknowledges the Chaos Emeralds' recent corruption, to which Applejack passive-aggressively starts fussing at him, telling him off for the attack. Upon nosily examining the corrupted Chaos Emeralds, and arguing with a cautious Applejack, Rainbow Dash is accidentally empowered by them and is transformed into a crazed super form the same as Sonic. Sonic takes action and pursues her as she takes off, much to Applejack's chagrin. Chasing Super Rainbow Dash across the landscape of Equestria, Sonic manages to catch up to Super Dash, but she struggles to get free of him, smashing him into rock fixtures, but Sonic holds on still. Resorting to flying upwards, creating a Sonic Rainboom, but the rising altitude doesn't deter him either. As they go higher, they begin icing over, and Sonic takes the opportunity to forcefully absorb the energy out of Rainbow Dash, depowering her and returning her to normal. The absorbed Chaos energy transforms Sonic into the original, good Super Sonic. He notices Rainbow having fallen unconscious and is currently falling to her death, and rushed after her to save her.
As Dash falls, the Mane Six arrive on the scene. They are terrified as Dash plummets, to which Super Sonic manages to catch her just in time, crashing in front of the girls. Emerging from the crater, Sonic carries Rainbow Dash, the two casually chatting. Applejack is about to attack Sonic, but Rainbow quickly defends him, explaining that despite what happened before, Sonic risked his life to save her. Just then, thanks to having aggravated his wounds from earlier, Sonic collapses again, much to Dash's horror.
Sonic finally wakes up again, this time in the Twilight's Treebury, where Twilight is starled by his awakening. Sonic is surprised Twilight has taken him in, beliving she and her friends despised him, apologizing for his actions. Twilight explains that Rainbow vouched for him since he saved her life, and understands that Sonic has no control over the new Super Sonic (aside from his brief moment of clarity). She also is confused over the dark corruption of the Emeralds, to which Sonic asks how she knows about them. Twilight sheepishly admits to her accidental mind reading, but explains that after the crazy debacle, she and Dash managed to convince the others to let her help him. Sonic is just exasperated and tired from the whole crazy experience he has gone through, and decides to talk to Twilight about it, only to see she has fallen asleep, and he does to.
Twilight later has a brief nightmare hazily showing Sonic and Eggman face to face amongst a burning Knothole Village. She is abruptly awoken by Spike, who's wondering why she's sleeping on the couch. She asks where Sonic is, to whom Spike states is cooking. Sonic greets Twilight with a good morning and explains he's cooking breakfast as a token of thanks for letting him crash with her, is the form of trays of blueberry and chocolate chip muffins. Twilight hastily states that she and him are late for a meeting with the Mane Six at Sugarcube Corner, bit Sonic tells her to chill out and eat, to which she eventually complies, while Spike is cramming his mouth full of muffins. After getting ready, a small awkward exchange occures when Twilight is giddy about having more muffins, but quickly tries to sound more formal, earning a laughing fit from both Sonic and Spike, before they head off.
On their way, Rainbow Dash greets them. She asks Sonic how he's doing, and Sonic engages in some playful banter with her, embarrassing her with caring suggestions, and calling her Skittles, explaining the reference, and Dash becomes fond of the candy's slogan. Suddenly, Pinkie Pie glomps Sonic out of nowhere. After hysterically trying to get her to stop biting him with the offer of jelly beans, Pinkie explains she's thanking him for saving Dash, and after Sonic asks her to do it less intensely, she bear hugs him instead, before they head into Sugarcube Corner.
Meanwhile, the Cutie Mark Crusaders are walking in the Everfree Forest, in another scheme to get their Cutie Marks. As their bickering with each other, they come across the path of wreckage (from Super Sonic's arrival) leading to Fluttershy's house. Suddenly, they come face to face with a Timberwolf. They obviously run for it, and the Timberwolf chases after them. At Sugarcube Corner, the Mane Six go over the debacle with Sonic's arrival, Applejack apologizing for her cold and hateful behavior towards Sonic, admitting that if not for Dash's urging, she would've left Sonic for dead, and Rarity apologizes for the same thing, which Sonic understands and dismisses. Sonic simply thanks them for letting bygones be bygones and helping him, but are interuptted by te sound of the CMC's screams. They rush outside to see the fillies being chased by the Timberwolf, to which Sonic immediately rushes into action. He Spin-Dashes into the wolf, destroying it, saving the girls. Scootaloo warns him of the the incoming danger of several other Timberwolves charging towards them. Sonic tells the fillies to follow him, threatening to carry them when Apple Bloom protests. Escorting them to safety with the Mane Six, Sonic engages the pack of Timberwolves. Despite their size, Sonic's trademark super speed easily destroys them. Then, the alpha Timberwolf shows up.