Sonic's story

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.
Upon returning to Soleanna, Sonic is attacked by a telekinetic hedgehog named Silver, who calls him the "Iblis Trigger" and tries to kill him, saying that it will protect the future. 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, 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 their 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 she was kidnapped. 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 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.


Shadow's story

Shadow's story begins one year after the events of Shadow the Hedgehog. Shadow infiltrates Dr. Eggman's base on a mission to find a missing agent, Rouge, who was sent to retrieve an artifact called the Scepter of Darkness. Upon finding and escaping with her, they are attacked by Eggman at a G.U.N extraction point in Kingdom Valley. During the attack, the Scepter of Darkness is shattered, releasing a being of darkness which absorbs Shadow's shadow and takes on his form. This being, Mephiles the Dark, appears to be familiar with Shadow, though Shadow has no memory of him. Mephiles proceeds to fling Shadow and Rouge to a devastated future.
Shadow and Rouge encounter Sonic, Tails and Knuckles, who were sent there by Eggman. 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 their Chaos Control together. While searching for Chaos Emeralds, Shadow and Rouge encounter Omega, who is on standby mode. After retrieving a pair of Chaos Emeralds, Sonic and Shadow create the space-time rift, allowing them to return to the present; however, Shadow spots Mephiles and remains in the future to confront him. In the present, Rouge finds Omega and gives him a Chaos Emerald, telling him to wait in time and assist Shadow. Back in the future, Shadow is told by Mephiles that humanity will use Shadow as a scapegoat for Iblis's misdeeds and imprison him, but he refuses to join Mephiles, who turns into a new, crystalline version of Shadow. Shadow and Mephiles battle until Omega appears a while later. With the help of Omega, Shadow defeats Mephiles and Mephiles escapes into the present while Shadow and Omega chases after him. Shadow goes off to find Eggman to learn more about Mephiles, while Rouge and Omega track down Mephiles themselves.
Shadow finds Sonic being attacked by Silver and saves him. Before battle, Silver mistakes Shadow as Mephiles. After battle, Shadow overpowers Silver with his use of Chaos Control, but Silver, in an attempt to strike back, takes out his Chaos Emerald and utilizes Chaos Control at the same time as Shadow, creating a time-space rift. In order to find answers to their respective questions, Shadow and Silver enter the rift and find themselves ten years in the past when the failure of the Solaris Project, an event known in the present to have caused great devastation, occurred. They arrive during an explosion that injures or kills all within its radius and releases Mephiles and a fiery being, Iblis, revealed to be two separate forms of the god Solaris. Armed with the Scepter of Darkness by the wounded Duke of Soleanna (Elise's father), Shadow chases after Mephiles and seals him within the Scepter. Having done what they needed to do, Shadow and Silver return to the present (leaving the Scepter of Darkness with Mephiles sealed in it behind).
Shadow reunites with Rouge and travels to Wave Ocean and finds Omega after defeating Mephiles. Omega has learned from Mephiles that he will be the one who captures Shadow in the future; however, Rouge comforts Shadow with the notion that she will always remain by his side. With a new Scepter of Darkness, Shadow, Rouge and Omega confront Mephiles and attempt to seal him away once more, but his new form prevents them from doing so. Using the power of the Chaos Emeralds, Mephiles clones himself into an army and reminds Shadow of humanity's betrayal in an effort to sway him to his side. Undeterred and unconvinced, Shadow takes his inhibitor rings off his gloves, and unleashes all the energy from within himself and begins his assault on Mephiles' army of clones with Rouge and Omega by his side.


Silver's story

Silver and his friend, Blaze the Cat, 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.
Upon reaching the past, Silver and Blaze are separated. While searching for Sonic, Silver meets Amy Rose. Silver and Amy help each other in their search for Sonic, though they are both unaware they are seeking out the same person, as well as what they plan to do with him. Upon finding Sonic, Silver attacks him, only to be stopped by Amy. Seeing how much Amy cares for Sonic makes Silver question his motives but, upon reuniting with Blaze, strengthens his resolve.
Infiltrating the base of Dr. Eggman, Silver recovers a Chaos Emerald and keeps it for himself. Silver encounters Sonic again, only to be stopped and attacked by Shadow. Shadow overpowers Silver with his use of Chaos Control, but Silver, in an attempt to strike back, takes out his Chaos Emerald and utilizes Chaos Control at the same time as Shadow, creating a rift in time and space. In order to find answers to their respective questions, Silver and Shadow enter the rift and find themselves ten years in the past when the failure of the Solaris Project (an event known in the present to have caused great devastation) occurred. 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"; not to mention the fact that the Iblis Trigger is to not be killed. 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 do not 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.


Last Story

When Sonic and Elise return to the forest, Mephiles appears out of nowhere, blinds them with the power of the purple Chaos Emerald, and projects an energy spear that impales Sonic through the back, seemingly killing him instantly. Elise cries in despair, releasing Iblis from within her. Shadow, Rouge and Omega have defeated Mephiles' clones but have forgotten about the real Mephiles. They see a Chaos Emerald on the floor which Shadow tries to take but it flashes and blinds their eyes. Using the power of his and the other six Chaos Emeralds (scattered around elsewhere), Mephiles absorbs Iblis and mutates into one single being, Solaris the Timereaver, the sun god worshipped by the residents of Soleanna, and creates a distorted world to destroy time itself. Elise, Shadow, Silver, Tails, Knuckles, Rouge, Omega, Amy, Eggman, and Sonic's body are caught in the space-time rift and gathered together.
After everyone mourns Sonic's apparent death, Eggman reveals that Solaris is to bring about the end of the world by destroying time itself. Everyone resolves to defeat Solaris, but Eggman informs them that Solaris exists in all timelines, and thus defeating it in the present time would do nothing. Refusing to give up, Silver suggests that they attack and destroy Solaris all at once, but Shadow deems such a feat impossible without Sonic. However, Elise feels Sonic's presence, and Silver deduces that they can revive him with the power of the seven Chaos Emeralds scattered all around the distorted world of time.
As reality itself falls apart around them, Sonic's friends venture across the distorted worlds and gather the seven Chaos Emeralds scattered throughout by Solaris. Using their power, along with her kiss, Elise brings Sonic back to life in the form of Super Sonic. He transfers his power to Shadow and Silver, turning them into their super forms as well, and together the three hedgehogs fight Solaris in a final battle and successfully defeat him, causing Solaris to be ripped apart and flung through space and time itself. Afterwards, Sonic and Elise travel back in time to the birth of the Flames of Disaster, realizing that if they put them out, Solaris will be erased from history, though they will never meet each other as a result. In despair, Elise begins to cry and shouts that she doesn't care what happens to the world as long as she and Sonic are together; though Sonic is clearly less-than-happy about this result as well, he knows what has to be done, and tells her to just smile, convincing her to blow out the flame.
Afterwards, time reboots back to the Festival of the Sun, though Eggman does not attack this time; all of the events that transpired beforehand, in effect, never happened. However, during the parade, Elise feels a familiar blue wind pass by her, and smiles. The scene cuts to Sonic on a rooftop, watching her and smiling. Both events indicate that Sonic and Elise have a recollection of the game's events to some extent.