The city of Soleanna is ruled by Princess Elise, who is the keeper of a dark secret, the "Flames of Disaster", which involves the Chaos Emeralds. The game opens with the citizens of Soleanna celebrating the Festival of the Sun; while lighting the ceremonial torch, Elise apparently suffers a terrifying hallucination of the city in flames with a demonic creature composed of molten magma in the center. As fireworks are launched, multiple missiles hit the ground around her, and Dr. Eggman arrives with a small army of robots. He reveals his intentions to kidnap Elise in order to obtain the secrets of the Flames of Disaster, who is, of course, unwilling to comply. At that moment, a circle of blue wind appears around them and the blue circle of wind revealed to be Sonic, who destroys a small number of Eggman's robots and escapes with Elise, while Eggman orders his robots to fire on him.
As Sonic escapes, the scene switches to the sight of a white-furred hedgehog named Silver, who speaks of finally locating the "Iblis Trigger". While running through the city, a confused Elise asks Sonic why he is helping her, but he replies that he has "no special reason". Soon afterward, more of Eggman's robots attack them, and Eggman successfully captures Elise in the Egg Mobile while Sonic is distracted fighting them. As Eggman returns to the Egg Carrier, Elise throws Sonic her Chaos Emerald, which he catches and assures her that he will rescue her. Unconcerned, Eggman simply decides to let Sonic hold onto "his" Emerald for the time being, and escapes on board the Egg Carrier as Sonic looks on.
The next morning, while attempting to gather information on Eggman's whereabouts, Sonic runs into Tails, who has apparently been helping to clean up the city after Eggman's attack. Tails reveals that he knows that Sonic had attempted to save Elise, and offers to help Sonic out however he can; while he doesn't know what Eggman's up to this time, he knows it isn't good.
Me: hun... that's new... I got-
Elise: oh you must be...
Me: i'm johnathon patrick James Rice. nice to meet you...
Eggman knock me out with zapper...
Eggman: that's not's nice to tresspass my base...
Sonic and Tails chase the Egg Carrier to Wave Ocean, a nearby beach, but are unable to catch up to it before it escapes. Defeated for now, Sonic and Tails decide to return to the city.
Sonic and Tails make their way to the Dusty Desert, where Eggman has been seen, and landing right in the room where he is keeping Elise, who is quite glad to see them (or at least Sonic). At that moment, Eggman arrives and unleashes his Egg Cerberus robot on them, which Sonic defeats. Afterwards, Eggman sends a massive amount of robots after them, and Tails creates a diversion in order to allow Sonic and Elise to escape unnoticed.
Sonic: um who are you..
Me: johnathon, johnathon Patrick Rice. and can we go before they coming to get us...
Tails: you coming with me johnathon... Now hang on...
me: for whaaaaaaaaaaaaaaaaaaaa
Sonic initially has the upper hand, but Silver catches him off-guard and psychokinetically throws him into a building, incapacitating him. Silver demands to know how someone as weak as Sonic could destroy the world; Sonic asks what he means, but Silver decides that it doesn't matter, as long as the "Iblis Trigger" is destroyed. However, Eggman capitalizes on Sonic's distraction to kidnap Elise again, and Sonic attempts to run after them, but Silver isn't about to let him run off. Silver knocks him down with his psychokinesis, and is about to deliver the coup de grace when Amy suddenly steps in. Silver somehow knows Amy, and orders her to move, but she isn't about to let him hurt Sonic any more. Sonic takes the opportunity, thanking Amy, and pursues after Eggman.
After a brief encounter with a group of Soleannan soldiers, who accept Sonic's help despite initial reluctance, Sonic enters the warehouse district of New City and meets up with Tails and Knuckles, the latter of whom gives him a holographic message that he received from Eggman. Eggman negotiates a deal; if Sonic comes to the White Acropolis and gives Eggman the Chaos Emerald that Elise had given him earlier, then Eggman will let Elise go without a fight. Though Tails and Knuckles are both positive that Eggman is setting up a trap, Sonic decides to go anyway, planning to "thank" Eggman for telling him Elise's whereabouts.
Sonic, Knuckles, and Tails fight through the White Acropolis and enter the room where Eggman and Elise are. Sonic obediently puts the Chaos Emerald onto a small pedestal, but, unsurprisingly, Eggman double-crosses the trio and activates a force field, trapping Team Sonic within. At that moment, Eggman activates his "Solaris prototype" (the name of which surprises Elise), and Sonic and co. vanish into thin air. The minute they vanish, Eggman assures Elise that Sonic, Tails, and Knuckles are still alive (for now), but have been transported to another time period; however, Eggman does not know where they ended up, as he needs a power that Elise apparently possesses and all seven Chaos Emeralds to fine-tune the machine.
Sonic, Tails and Knuckles encounter Shadow and Rouge, who are also trapped in this future. In order to return to the present, they need to create a rift in time and space, which they figure can be created if Sonic and Shadow use Chaos Control together. While searching for Chaos Emeralds, Sonic, Tails and Knuckles encounter Silver, his friend Blaze, and Mephiles, a dark being who resembles Shadow, tells Silver that Sonic is the one responsible for the future's devastation, and takes them back in time to kill Sonic. Sonic learns from a computer file that Elise was killed when Eggman's battleship exploded two days after the Festival of the Sun. After retrieving a pair of Chaos Emeralds, Sonic and Shadow create the space-time rift, allowing them to return to the present.
Sonic returns for Elise, but is once again attacked by Silver, also allowing Eggman to kidnap Elise yet again. Fortunately, Shadow arrives to confront Silver, allowing Sonic to rescue Elise, and he returns her to her castle in Soleanna. Later, Eggman arrives in his battleship and threatens to destroy Soleanna, and Elise willingly surrenders herself to him to protect her people. Eggman explains to Elise that in order for his plan to take over the world to work, he requires the seven Chaos Emeralds and the dormant power of the Flames of Disaster within Elise to awaken Solaris, allowing him to harness the sun god's power over time.
On his way to rescue Elise, Sonic encounters Silver once more who, instead of attacking him, expresses concern for Elise as well. The two hedgehogs team up, but before they reach the battleship, it malfunctions, crashes and explodes, just as Sonic feared while back at the future. However, Sonic and Silver realize they can use Chaos Control to travel back in time to the previous day, before Eggman's battleship launched. Sonic travels to the past alone and reunites with Elise. Defeating Eggman (who battles Sonic with the Egg Wyvern) one last time, Sonic escapes the exploding battleship with Elise and makes it back to solid ground.