Silver and his friend, Blaze, live 200 years in a devastated future, their time period destroyed by an immortal creature called Iblis, the Flames of Disaster. Despairing over the fact that they have no way to truly defeat Iblis, Silver and Blaze encounter a mysterious being named Mephiles, who claims that he can stop the Flames of Disaster by destroying the "Iblis Trigger," a being who will unleash Iblis. Mephiles points out the Iblis Trigger to be none other than Sonic, and he sends Silver and Blaze to Sonic's time period.
They arrive during an explosion that injures or kills all within its radius and releases Mephiles and Iblis, revealed to be two separate forms of the god Solaris. Silver chases after Iblis, who is sealed away by the King of Soleanna into the body of his daughter, Princess Elise, with a Chaos Emerald. Before he succumbs to his injuries from the explosion, the King tells his unconscious daughter to never cry, as it would unleash Iblis. Silver then realizes that Mephiles has tricked him and that Elise is the "Iblis Trigger". Before returning to the present with Shadow, Silver gives his Chaos Emerald to Elise.
Realizing that Sonic isn't the Iblis Trigger, Silver is informed by Blaze that Princess Elise has surrendered to Eggman and was taken away on his battleship. Silver and Blaze fear that Eggman plans to release Iblis. On his way to rescue Elise, Silver encounters Sonic and teams up with him. Before they can reach Eggman's battleship, it crashes and explodes due to a system malfunction. Silver and Sonic use Chaos Control to travel back to before when Eggman's ship launched. Sonic travels to the past alone to save Elise from her grim fate, but not before giving Silver a Chaos Emerald.
Silver and Blaze return to their timeline in an effort to stop Iblis, now knowing they don't have to alter the past to save the future. Finally defeating Iblis, Silver attempts to seal the Flames of Disaster away into his soul, but he is rejected. Blaze offers herself as the vessel for Iblis and is sealed away to another dimension, finally restoring peace to their time.
Princess Elise is the beloved ruler of the peaceful city of Soleanna. During the Festival of the Sun, the city is attacked by Doctor Eggman who is seeking the secret to a powerful weapon, the "Flames of Disaster," that will help him take over the world, which Elise possesses. However, Sonic arrives and helps Elise escape, though Eggman quickly tracks him down, sends more robots to attack them, and successfully captures Elise while Sonic is preoccupied. Before being taken away, Elise gives Sonic her Chaos Emerald.
The next morning, Sonic meets up with Tails and sets out to find Elise. Before long, Sonic manages to rescue her, and Tails splits up with Sonic to divert the attention of Eggman's robots. Noticing Sonic got hurt, she blames herself for it. Sonic tells her to smile and that her smile is all he needs. Elise then explains to Sonic that the Flames of Disaster Eggman hopes to unleash is the fury of Solaris, a sun god her people worship, and that she holds the secret to this power.
While Sonic and Silver fight, Elise is once again kidnapped by Eggman. Amy arrives out of nowhere and prevents Silver from finishing off Sonic, allowing Sonic to chase after Elise, thanking her briefly. Sonic reunites with Tails and finds Knuckles at the Warehouse of New City with a message from Eggman, and the three head over to Eggman's base in White Acropolis, where Elise is being held. There Sonic agrees to give him his Chaos Emerald in exchange for Elise but, unsurprisingly, Eggman goes back on his promise and traps the trio in a time machine, which thrusts them into a distant, post-apocalyptic future. Sonic learns from a computer file that Elise was killed when Eggman's battleship exploded two days after she was kidnapped.
Sonic returns for Elise, but is once again attacked by Silver, also allowing Eggman to kidnap Elise again. Fortunately, Shadow arrives to confront Silver, allowing Sonic to rescue Elise.
After running through the jungle, Sonic tells Elise she should return to the castle. Elise agrees to do so, but shows sadness over this. Noticing her sadness, Sonic takes her to a lake. Elise is captivated by the scenery. She then asks Sonic that once he defeats Eggman, will he leave the city, to which Sonic nods. She tells him that she enjoyed experiencing the adventure, and requests to him that when he leaves the city, that he remember it. Sonic promises her that he will. Elise suddenly turns away from Sonic, fighting back tears. She tells herself that she must not cry and swiftly turns back to Sonic, hugging him. As Sonic returns her hug, he once again gently tells her to smile. Elise regains her composure and nods.
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, but instead of attacking Sonic, 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. 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 one last time, Sonic escapes the exploding battleship with Elise.