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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, among other familiar faces.
The story has a similar premise to Gunflame345's popular fanfic A New Dawn, another crossover between Sonic and MLP that invovles disastrous consequences leading to Sonic being transported to Equestria, serious and mature themes, violence and discrimination against outworlders (although, it could be noted that A New Dawn is far darker than Chaos in Equestria, playing into sex, war, graphic violence and a generally cynical, realistic atmosphere, where Chaos in Equestria leans closer to the canonical lighthearted and upbeat tone of both series).
The story has received positive reception and has been well-received by fans. Much of the artwork are commissions by other deviants. The story received an immediate sequel titled Sonic: Battle for Equestria. A comic adaptation is underway, written by TheMarioFan8881.
Opening on Mobius starts with Sonic the Hedgehog and his friends, Miles "Tails" Prower, Knuckles the Echidna, and Amy Rose in an aerial firefight with the Egg Carrier. Eventually avoiding the Badniks and enemy fire, they forcefully board the ship. Fighting through the defenses, they soon confront 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. Unfortunately, the technology (the same used on Super Sonic in Sonic Unleashed) apparently proves fatal, appearing to kill Tails, Knuckles, Amy, Cream, Shadow and Rouge. Disappointed at their deaths, Eggman callously mocks Sonic over it. Utterly horrified and enraged, Sonic violently tears through the ship at top speed, vowing to kill Eggman 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 once again mocks Sonic over having killed his friends. Sonic, in barely held back fury, violently attacks Eggman, beating the scientist across the control room, culminating in savagely crippling his nemesis. Despite immense, debilitating pain, Eggman sadistically eggs Sonic on. 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). Finally scaring Eggman, he attempts to escape in his Egg Mobile. Super Sonic pursues, sadistically intent on killing him, seizing him and savagely beating him again. Eggman unsuccessfully begs for his life, but Super Sonic throws it back in his face, stating killing him would be avenging the countless victims of the mad doctor's multiple conquests. In one final desperate move, Eggman activates a weapon known as the Lethargy Laser (a portal-generating machine). The resulting portal pulls Super Sonic into it, leaving Eggman to black out from his injuries as the damaged Egg Carrier drops out of the sky. Before cutting away, the Lethargy Laser's power grid malfunctions as purple energies begin surging through the ship.
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 latch on to her, 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 states that Sonic 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, to which Sonic and him tease Twilight for her compulsive and overtly formal demeanor before leaving.
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 nicknames her Skittles for her chromatic hair. 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. Running in terror, 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, to which Rarity adds in, to which Sonic understands and dismisses, thanking them for showing him compassion instead, but is interrupted by screams.
They rush outside to see the Crusaders being chased by the Timberwolf, to which Sonic immediately rushes into action. He saves them by spin-dashing into the beast, destroying it. 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. The alpha attacks Sonic, but after realizing the wood that makes up it's being is too thick, opts to use his Blue Cyclone move to obliterate it. The Mane Six and the CMC arrive too late to witness the battle, disappointed. Heading back into town, they find themselves being stared down by the populace. One particular stallion steps up, rudely questions Sonic's presence, but is interrupted by the Crusaders, who angrily defend Sonic. Thankfully, Mayor Mare steps in to express graditude to Sonic for having selflessly fended off the Timberwolves.