Sonic the Hedgehog 2006 is split into four stories - Sonic's Story, Shadow's Story, Silver's Story, and the Last Story.
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 the Chaos Emerald, which he catches and assures her that he will rescue her. Eggman tells Sonic to hold onto the 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 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. 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 an army of robots after them, and Tails decides to distract them in order to allow Sonic and Elise to escape unnoticed. After escaping the desert and entering the plains, Sonic comes to a stop. Elise thanks Sonic for his help, but then notices a wound on his arm. Despite Sonic's insistence that he's fine, Elise bandages his arm with a handkerchief. Blaming herself for Sonic getting hurt, Elise apologizes, but Sonic merely tells her to smile, stating that her smile is all he needs to keep him going. While walking through the plains, Elise fills Sonic in about the Flames of Disaster, Solaris (the sun god honored by Soleanna), how they had nearly faced the full force of his anger ten years ago, and how she had lost her father in the incident, and fears what would happen if Eggman makes history repeat itself. Without warning, Sonic grabs Elise's hand and runs through the plains with her. Afterwards, Elise lightens up, and Sonic gives her some useful advice.
However, upon their return to the city, Sonic and Elise are attacked by Silver, who claims that Sonic's actions will condemn the world, and they battle. 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 why Sonic would 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. 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 finish him off when Amy suddenly steps in. Silver orders Amy to get out of the way, but Amy refuses. Sonic takes the opportunity, thanking Amy, and pursues after Eggman.
Sonic and Tails enters the warehouse district of New City and meets up with Knuckles, who 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 assume that Eggman is setting up a trap, Sonic decides to go anyway, planning to "thank" Eggman for telling him Elise's whereabouts.
The trio fight through the White Acropolis and enter the room where Eggman and Elise are. Sonic 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 aren't dead (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 arrive to the distant future and meet Shadow and Rouge, who are also trapped as well. 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 sees Silver, his friend Blaze, and Mephiles, a dark being who resembles Shadow. Mephiles tells Silver that Sonic is the one responsible for the future's devastation, and takes them back in time to kill Sonic. The trio heads inside the computer room and they learn from a computer file that Elise was killed when Eggman's battleship exploded two days after the Festival of the Sun.
In the Flame Core, Sonic, Tails, and Knuckles find Shadow and Rouge who found a Chaos Emerald. Rouge brags about finding it and makes a snide comment about Knuckles, making the echidna indignant. Tails informs the crew that another Chaos Emerald is located inside the volcano, so they all head inside. Before finding the Emerald, Iblis appears out of nowhere. Sonic fights it off. After the battle, Sonic and Shadow use the two respective Chaos Emeralds to perform Chaos Control, opening a time rift. Sonic, Tails, and Knuckles got inside, while Shadow and Rouge turn their attention to something, but that's another story.
Team Sonic returns to the present, and spot a newspaper. Reading upon it, Elise has been kidnapped again. Sonic races through Radical Train and rescues Elise from Eggman's train, but is once again attacked by Silver, also allowing Eggman to kidnap Elise yet again. Fortunately, Shadow arrives to confront Silver, allowing Sonic to go and rescue Elise. As Elise refuses to comply to Eggman's demands, she jumps off of the aircraft, but Sonic jumps and captures her safely. Angered, Eggman sends out the Egg Genesis to battle Sonic. After defeating the giant robot, Sonic takes Elise to Tropical Jungle away from an army of Eggman's robots.
As Sonic and Elise are clear away from the robots, they arrive to a lush jungle. Elise tells Sonic that she enjoyed the adventure with him. Knowing that Sonic will leave, Elise tries to prevent crying and glomps Sonic, who tells her to smile. After Sonic returns Elise to her castle in Soleanna, Eggman arrives in his battleship and threatens to destroy the city, 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 a group of robots until Silver came and destroyed them. Sonic becomes suspicious towards Silver, but he explains that "circumstances have changed" and expresses concern for Elise as well. The two hedgehogs team up and head to Kingdom Valley. Before they reach the battleship, it malfunctions, crashes and explodes, just as Sonic feared while back at the future. However, Silver realizes they can use Chaos Control to travel back in time to the previous day, before Eggman's battleship launched. Both hedgehogs use Chaos Control to open a time rift. Sonic thanks Silver and travels to the past alone.Sonic arrives to an earlier point of time and enters Aquatic Base with the help of Tails and Knuckles. He arrives to the launching site of the Egg Carrier and lands on it. With the Egg Carrier later malfunctioning, Sonic arrives and reunites with Elise. Furious over this, Eggman seeks to defeat Sonic with his Egg Wyvern. After defeating Eggman one last time, Sonic escapes the exploding battleship with Elise and makes it back to solid ground. They had a good laugh over it and Sonic commends Elise smiling. The two then enjoy the view of the sky.
The two arrive to a room and Rouge asks Shadow to take her to the rendezvous point in Kingdom Valley. After arriving there, Shadow and Rouge are confronted by Dr. Eggman, who demands to retrieve his stolen property. Eggman's robots swoop down to attack, and in the heat of the battle, the Scepter of Darkness is completely shattered. With the seal destroyed, a shade is freed. Resurrected in the likeness of Shadow through his shade, Mephiles the Dark introduces himself and hints at a past history the two share. Mephiles, using a time warp similar to Chaos Control, flings Shadow and Rouge to a future on the brink of collapse.
When they arrive, Shadow and Rouge discover on the readings of a computer that they are 200 years in the future. Afterwards, they meet up with Sonic, Tails, and Knuckles, who were sent to the future by Eggman's latest machine. Sonic and Shadow conclude that they must use Chaos Control to get home, but first must find the Chaos Emeralds. Shadow and Rouge manage to find a Chaos Emerald, but along the way, they find an inactive, dusty E-123 Omega, lying in stand-by mode for hundreds of years for an unknown reason. The two arrive to the Flame Core and are later meet by Team Sonic who had discovered that the next Emerald is located inside the volcano. The group head inside in pursuit of the Emerald and are confronted by with Iblis. Shadow defeats it, and he and Sonic use the Chaos Emeralds to use Chaos Control to create a time warp. Sonic and company go back to their time, except for Shadow, who stays to confront Mephiles.
Upon catching up with Mephiles, he reveals to Shadow that humanity, looking for someone to blame for the destruction of the Earth, saw Shadow responsible for the catastrophe; he tells Shadow that he was hunted down, defeated, and trapped behind an energy seal. Mephiles tempts Shadow to join him to gain vengeance upon the humans, but Shadow refuses, declaring that he determines his own destiny, at which point Mephiles transforms into his second form, a more powerful crystalline monster, and the two engage in battle.
Meanwhile in the present, Rouge realizes that Shadow is alone in the future fighting Mephiles, without a Chaos Emerald. She searches for E-123 Omega in Tropical Jungle, gives him a Chaos Emerald, and tells him to sit and wait in stand-by mode until the distant future becomes the present, and to assist Shadow fighting Mephiles. Shadow, at Mephiles' mercy, is rescued by Omega, who gives him the Chaos Emerald and helps Shadow fight Mephiles. Defeated, Mephiles flees to the present through a time warp and Shadow and Omega follow him to the present.
Omega pursues Mephiles, and Shadow finds Rouge, who informs him that Dr. Eggman is apparently searching for him. Shadow concludes that Eggman is searching for Mephiles, and goes to interview the doctor. Upon locating Eggman's train around Radical Train, Eggman tells him that, to understand why he wants Mephiles, Shadow must know about the accident that happened 10 years ago, the Solaris Project.
Shadow then leaves only to find Sonic, who is under attack by Silver. Shadow rescues Sonic, who runs away with Princess Elise, and Shadow engages in a fight with Silver. Shadow is able to overcome the telekinetic hedgehog by freezing time and kicking him in the head for good measure. Refusing to accept defeat, Silver also induces Chaos Control, much to Shadow's shock. Silver tells him that he must go and kill Sonic to save the future. Realizing what he mean, Shadow tells Silver that in order to understand more about Mephiles and Iblis, they would have to use the warp and witness the accident themselves. So the two of them, using the Emeralds, open a time warp to 10 years ago - the Solaris Project.
They witness the Solaris Project's failure at hand, and watch as Iblis and the original Mephiles, a dark puddle, emerge, opening Silver's eyes to Mephiles' deception. The Duke of Soleanna tells them that the demons must be sealed, so he gives Shadow the Scepter of Darkness. Shadow goes to capture Mephiles, and Silver goes to capture Iblis. It is here that Shadow finds out why Mephiles knows him; it was Shadow who sealed him in the Scepter of Darkness in the first place. With Mephiles and Iblis sealed, Shadow leaves the Scepter in the past since he knew where it would end up in the present day. Silver and Shadow return and Shadow rushes off to find Rouge to tell her what he learned about Mephiles. Shadow finds Rouge and tells her to find out what the Scepter of Darkness, Mephiles' seal, was made of, so they can create another one.
Elsewhere, Omega has found Mephiles on Wave Ocean and defeats him once again, but Mephiles laughs and tells Omega that the reason he can defeat him so easily is because he was built to defeat Shadow later on. Omega refuses to acknowledge the truth at first but after Mephiles escapes again, he admits to Shadow and Rouge that he was the one that sealed Shadow in the future. He then comes to the conclusion that when something (or someone for that matter) becomes too powerful, it becomes a threat, and thus the world turns against it. Rouge then tells Shadow that he'll stand by his side, even if the world will turn against him.
At Dusty Desert, Shadow, Omega, and Rouge chase Mephiles to a desert temple with a new Scepter of Darkness, but Mephiles has already found a Chaos Emerald. After Shadow fights him and gains victory, Mephiles reverts back into his original form, a puddle of darkness. Shadow attempts to seal him in the new Scepter of Darkness, but it shatters and Mephiles is able to free himself. Mephiles reveals that what worked ten years ago no longer does because he is using Shadow's form. Mephiles uses his powers to summon a giant clone army of himself and he attempts, once again, to convince Shadow that he is a fool for protect those who will eventually seal him away. In response, Shadow replies, "If the world chooses to become my enemy, I will fight like I always have!" Mirroring a similar ability from Sonic X, Shadow removes his Inhibitor Rings and in a huge burst of energy, defeats the Mephiles clones with his allies by his side and the story ends as a cliffhanger.
Upon reaching the present day in a forest, Silver realizes that he got separated from Mephiles and Blaze and, elsewhere in Wave Ocean, Blaze makes the same realization. When Silver has his sights finally set on Sonic, he is interrupted by Amy, who mistakes him for Sonic. Amy quickly develops a friendship with Silver, and she promises to help him find who he is looking for, not realizing that he plans on finding and killing Sonic. They search for him throughout Dusty Desert and then return to the city, where Silver finds Sonic and engages him in a fight. Just before Silver could finish off Sonic, he is saved by Amy. While Sonic runs off to save Elise from the clutches of Eggman, Amy calls out Silver for trying to kill Sonic, but Silver says that he's responsible for the destruction of the future. Upset at this suggestion, Amy states she would choose Sonic over the world. Silver is left confused.
Somewhere else in the city, Silver is sitting on a bench, thinking of what Amy had said. Blaze finds him, Silver asks her whether or not is it right to kill someone to save the world. Blaze replies that she couldn't answer the question and reminds him that they must save the future. To find more answers, Silver and Blaze decide that Sonic is after Eggman, so they'll go after him too, hoping to get information. Upon arriving at White Acropolis, Silver and Blaze encounter the Egg Genesis obstructing their way. Silver defeats it and he and Blaze acquire a Chaos Emerald. Blaze explains that the Emerald changes thoughts into power and advises him to keep it as a "lucky charm".
Returning to the city, Silver and Blaze find Mephiles, who tells him that Sonic is at the terminal station. Silver heads to Radical Train and fights Sonic again, only to have Shadow save Sonic just as Silver was about to finish him off. Silver mistakes Shadow for Mephiles and Shadow corrects him. The two battle it out and induce Chaos Control using the two Chaos Emeralds they have in their possession. Shadow tells Silver that Mephiles is deceiving him and that they must head inside the time rift 10 years to the past to discover the origins of Mephiles and Iblis.
Silver and Shadow arrive at the perfect moment, during the explosion that releases Mephiles and Iblis in the first place and, ultimately, causes the Duke of Soleanna's death. Shadow seals the original Mephiles in the Scepter of Darkness and Silver learns that to defeat Iblis, they must seal him inside someone's soul, making that person into a sort of vessel; Elise was chosen as his host. Silver also learns more of Mephiles' intentions and discerns that he lied to him about Sonic being the Iblis Trigger. He meets with Shadow and the two return to the present. Before leaving, Silver gives a young Elise the blue Chaos Emerald, telling her to keep it as a "lucky charm", similar to what Blaze said to him.
Upon returning to the present, he meets up with Blaze, shares his findings and has a change of heart, resolving to help Sonic save Elise. As Sonic is confronted by an army of Eggman's robots, Silver comes to the rescue and destroys them. Silver explains to Sonic that there was a misunderstanding and offers to help him rescue Elise, and thus the two hedgehogs head to Kingdom Valley. Unfortunately, Sonic, Silver and Blaze arrive too late, as they watch the Egg Carrier explode causing the death of Elise and possibly Eggman as well. Silver then tells Sonic that if they use Chaos Control, Sonic can save Elise. The two hedgehogs use Chaos Control to open the time rift. Sonic rushes into the past to save Elise and gives Silver a Chaos Emerald for him to return to the future.
After journeying back to the future, resolved to finally defeat Iblis, Silver and Blaze search for Iblis in Flame Core and found Iblis and successfully defeat him. When Silver tries to seal him, though, by using himself as a vessel, Silver is unable to use himself as a vessel to seal Iblis. As the ultimate sacrifice, Blaze uses herself as the vessel, sealing both herself and Iblis into another dimension to save both Silver and her world. Disturbed over the loss of a good friend, Silver becomes upset, unsure if what he had set out to do was worth what he had to pay in the end. Nevertheless, light returns to Silver's world, and the game ends with him glaring at the Chaos Emeralds while Blaze is sealed with Iblis in another dimension.
Continuing from where Shadow's story ended, he, Rouge, and Omega recover from their battle with the Mephiles clones and Shadow notices the green and yellow Chaos Emeralds that Mephiles left behind. These create a blinding flash that send Shadow, Rouge and Omega to the time-space rift formed by Solaris.
Meanwhile, in Soleanna, Amy, Tails and Knuckles notice a large bright light that engulfs the city. When the light fades, they realize that they have also been transported to the rift where all of the previous levels in the game exist. Amy is the first to spot Silver, who has been teleported here as well by the Chaos Emeralds that Blaze used to seal Iblis within her. Everyone notices that they have all been brought to this strange place, even Dr. Eggman. As they try to understand what was happening, Dr. Eggman reveals that Iblis' seal has been broken. It is then that they turn and see Elise, cradling Sonic's body in her arms. Everyone was distraught and saddened that the blue hero is gone. Eggman explains that Mephiles reunited with Iblis by killing Sonic in order to make Elise cry; this fact made Silver realize why Mephiles wanted him to kill Sonic in the first place.
Eggman reveals that Solaris is about to bring about the end of the world by destroying time itself, and that, being a transcendental life form, it cannot be defeated in the present as it exists in all timelines, so defeating it in the present would do nothing. Silver refuses to give up, and suggests that they team up and destroy Solaris in the past, present and future all at once, but Shadow quickly shoots that possibility down, stating that, with Sonic dead, Solaris is completely unstoppable.
With Amy upset over Sonic's death and their impending doom, Elise recognizes a familiar wind in the air that makes her come to believe that Sonic may not be entirely dead yet. Silver, furthering Elise's observations, explains that they can use the Chaos Emeralds to revive him. The crew went to search for the Emeralds. All 7 Emeralds were discovered in 7 different locations; Tails finds the first Emerald in Crisis City; Omega finds a second one in Flame Core; Knuckles finds the third one in Tropical Jungle; Silver finds the fourth one in Dusty Desert; Rouge finds the fifth one in Wave Ocean; Amy finds the sixth Emerald in White Acropolis; and lastly, Shadow finds the seventh one in Kingdom Valley.
As the Emeralds were gathered, Elise says the prayer to revive Sonic; she also plants a kiss on him, thus transforming him into Super Sonic. Super Sonic thanks Elise and everyone is relived to see him alive. Super Sonic uses his power to transform Shadow and Silver into their Super Forms. Together, the three hedgehogs fight Solaris. The three use Chaos Control on Solaris causing the monster to be torn apart in a time loop. Everyone cheered as the three hedgehogs returned from defeating Solaris.
Sonic, now back to normal, travels with Elise to a point in the past where they find the "Flames of Disaster" and its birth. Elise realizes that if she puts out the Flames, Solaris will never exist, but she and Sonic will never meet each other. Overcome with despair, Elise begins to cry and shouts that she does not care what happens to the world as long as she and Sonic are friends. Though Sonic is clearly unhappy about this as well, he tells Elise to just smile and manages to convince her to abandon their meeting. She confidently puts out the Flames, eliminating Solaris from existence once and for all...
Time reboots back to the Festival of the Sun; this time, Eggman does not attack. In effect, none of the game's events exist anymore. Elise is in her boat waving the audience as Sonic runs through the public, the "wind" of his speed making Elise lose one of the feathers in her hair. A maid asks her if everything is alright, and Elise says that she thought someone was calling her. Another maid replies that it's just the wind, and Elise says that it might be, but that it felt familiar somehow, and smiles, apparently knowing who it was. She continues with the festival as Sonic watches from a rooftop. The game ends with Sonic watching Elise's feather flying into the night, also smiling.
Excluding the ending cutscene, the events of the game are thus erased from the Sonic the Hedgehog series' timeline.