(1) After the failed attemped to control the ancient technology on Starfall Islands which leads to terrible consenquences, Dr. Eggman as well as Sonic and all of his friends who have arrived to stop him are blasted and engulfed by the power of the technology which kills most of them while forcing Sonic out into the forest, being the only survivor yet losing all of his memories as a result. A ghostly form of Amy Rose, only being able to link herself into the amnesic Sonic to hopefully help him to regain his memories as he wakes up confused on who he is, and is uncertain if his name really is Sonic, is soon corrupted by a mysterious form of an Athoma girl as well as Sage, the A.I Eggman attempted to place into the technology, and tricks Sonic into developing new powers called the Cyberboost.
She, disguising herself as Amy, helps Sonic to re-learn his previous abilities as well as gain new ones while attempting to escape from the newly awakened technology which, according to legend, was what actually helped to learn the first known knowledge of the Chaos Emeralds which are needed to fight against Titans, giant robotic machines that were used by the 'gods' who used the machines to destroy all early known humans through out Starfall Islands before they could advance in a dangerous rate and warns that Sonic will meet the same fate and his friends are doomed to remain trapped inside Cyberspace. Using his old and new abilities to travel through the long forgotten landscapes while being guided by 'Amy', Sonic slowly remembers his past while is haunted by the ghosts of his friends who are distraught that he lost his memories but encourage him to keep going.
Finding Cyberspace forms of Chaos Emeralds to fight each Titan, Sonic gradually recalls his memories, including his instant distrust in the ghost of Eggman who attempts to use his amnesia to his advantage and take over his body but fails. Sonic also learns more about the past of Starfall Islands and realizes that the Islands hail from another world, a human world and that the human civilization on Earth actually migrated from another Earth during an apoclypse which forced them to abandon the old Earth for a new home where they used Starfall Islands as a sanctuary, before the events of the Cyberspace crisis forced them to move elsewhere around the world and eventually learn to co-exist with the advanced animals.
While attempting to rescue and reconnect with his friends, Sonic soon becomes distraught when he realizes that he can only save their ghostly forms from Cyberspace for them to move on and not being able to revive them unless he makes a catastrophic decision which would result in worlds and realities colliding and causing the universe to shatter into multiple realities. Discouraged and believing that he is responsible for the terrible event that killed his friends while attempting to stop Eggman, Sonic begins to lose hope as he remembers more about them while fighting more Titans and collecting the Chaos Emeralds. Despite his friends' encouragments for him to keep going and that they would always watch over him, Sonic feels like he cannot live on even with new friends during his journey such as Bobo and Cosmos, who attempt to keep him company but fail to heal his guilt-ridden heart, and wonders if he should trust Amy who, breaking through the ghost girl's/sage's influence, attempts to tell him not to trust the ghost/A.I but is repeatedly blocked.
Eventually after defeating the final Titan, Sonic attempts to free Amy's soul, but instead the Ghost girl/Sage takes over and reveals that she used him in order to destroy the Titans to fully awaken the technology to seek revenge against the Cyberlords and reshape reality into her own image, trapping all of the souls of Sonic's friends just as his memories fully return. Attempting to use the Chaos Emeralds, reality soon shifts and begins to collide with other worlds which is destroying them quickly. Now left with no other choice but to destroy Sage and create the new mulitverse, Sonic transforms into Hyper/Ultra Sonic and defeats Sage at the cost of his friends and his world, before blacking out as everything shatters, forming into the Shatterverse.
In the post-credits scene, Sonic awakens with new gloves and shoes in a world of the Eggmanland Empire where he is faced with four duplicants of Eggman himself as well as a new version of Tails, now having nine tails instead of two and is grown up, informing him that in order restore everything back to normal, Sonic must go into new shattered realities and defeat the Eggmen. Wishing to learn more about his own worthy as well as redeem himself for his actions, Sonic immediately agrees and sets forth on his new adventure, setting stage for the TV series of Sonic Prime.
(2) Similar to the first summary, Sonic's friends and Eggman become trapped within the Cyberspace while Sonic is left alone on Starfall Islands in a coma where he awakens hundreds/thousands of years later in suspended animation with amnesia, and is guided by a mysterious ghost girl(Sage in disguise) who intimidates Amy's voice in order to trick him into locating the Chaos Emeralds as well as freeing his friends and defeating the robotic Titans.
Gradually Sonic regains his memories and soon begins to feel uncertain on whether or not he should trust 'Amy'. As like in the previous story but with his friends rescued yet recaptured, Sonic is forced to create the shatterverse in order to save everyone as a last resort, still lacking most of his memories and how with a new version of Tails, seeks to save everyone and redeem himself for his actions, leading into Sonic Prime.
(3) Like the second summary, everyone except Sonic are trapped in Cyberspace while he loses his memories and is guided by Amy who, with her psychic abilities, helps him remember everything while searching for the Chaos Emeralds as well as rescue everyone through out each Cyberspace Zones and battle against the Titans. Yet Sage controls the robots to stop him with Eggman secretly taking control and in the end once Sonic regains his memories and is able to save his friends, fights the evil duo only for worlds to collide and soon creates the shatterverse, separating Sonic from his friends and forcing him to explore the new world in order to return everything back to normal, leading into the canon events of Sonic Prime.
(4) Similar to the first and third summaries, Sonic is rendered with amnesia while his friends become trapped inside the Cyberspace and giant robots known as Titans which hold the Chaos Emeralds. Guided by the spirit of a pink haired human woman who resembles to Amy on Starfall Islands, she helps guide him along the way across the land that was once the home of hedgehogs and a human expedition arrived to study the technology that was creating the Chaos Emeralds, but a terrible tragedy happened which left most fleeing for their lives thousands of years ago. Along the way, as he fights the Titans as Super Sonic(or not), he rescues his friends who are shocked to learn that he doesn't recognize them. The situtiation gets worse when Sonic had rescued Eggman who, realizing this as well, tricks Sonic into thinking that he is also a friend and destined to rule the world while his friends are his enemies.
Uncertain by this, gradually Sonic's memories return as he rescues more of his old companions but has a hard time believing whether his memories are real or not as Eggman has also been manipulating the Cyberspace each time Sonic goes in to grant him fake memories which is causing tensions between him and his allies and being forced to fight Knuckles. The image of Amy however begins to trigger Sonic's real memories and that the ghost girl may also have been manipulating him. Gaining the last of his friends and the final Chaos Emeralds, Eggman takes control and tricks Sonic into thinking he is a creation and that "Sonic the Hedgehog" never existed and recaptures his friends, saying that they are also fake.
Distraught, Sonic runs away in anger and sorrow bracing himself to live as Eggman's slave. But as he does while attempting to throw away the Chaos Emeralds without knowing who to trust, the ghost of Amy(who has been killed) restores his real memories including what happened to the point of when he was rendered with Amnesia. Devastated and guilt-ridden with having been tricked and at Amy's death, Sonic vows to save his friends and the world once again. He hurries back and fights Eggman, the Colossus Titan and the Pink Haired A.I who is revealed to be Sage and then takes over the machine while disavowing Eggman. Saving his friends once again and transforming into Super Sonic, he breaks the shell core of the Titan and rescue's Amy's body, which has been used as fuel as it is revealed she is the descendant of the hedgehogs of Starfall Islands. This leads to two endings.
The Canon Ending is much like the previous story endings to which Sonic is forced to create the Shatterverse to save the worlds as Space and Time begins to collapse and must now go on a new journey which leads to the events of Sonic Prime.
The Good but non-canon Ending has Sonic instead sacrifice himself by reviving Amy, returning her soul to her body and destroying Sage and the Titans, eliminating all technology of Starfall Islands. As his friends mourn Sonic's death despite having saved them and saving Space and Time, their tears and wishes cause the Chaos Emeralds to revive him with his memories intact and they all embrace. Now no longer taking his friends for granted, Sonic happily rejoices by the fact that he is real and so are his loved ones and they all leave Starfall Islands while Eggman is left stranded on an isolated Island.
And also multiple endings for the game, similar to Shadow the Hedgehog.
First Ending: Sonic manages to defeat the ghost girl/Sage, but is forced to say goodbye to his friends who move on to the afterlife, wishing him to stay positive and that they would always watch over him. But instead he becomes depressed and, feeling guilty for his actions and failure to revive them, decides to remain on Starfall Islands for the rest of his life as he is unable to move on as punishment for his misguidence, ending the Sonic Franchise all together.
Second Ending: Similar to the first ending, Sonic says his goodbyes to his deceased friends and leaves Starfall Islands in guilt and sorrow despite Bobo and Cosmos attempting to comfort him to keep him company. He then runs through the desert of the mainland where he sees stars take shape of his friends, similar to the Bad Ending of the GB version of Sonic 2 where Tails has been killed by Dr. Robotnik. He tearfully cries and runs away into the distance. His whereabouts remain unknown.
Third/Fourth Ending: As Sonic fights and defeats Sage/Eggman while attempting to rescue his friends, the whole of reality collapses which forces him to use the Chaos Emeralds into creating a new Multiverse known as the Shatterverse where everybody is sent to different realities and timelines with their memories of their previous lives lost as a result. Guilt ridden, and finding himself in an Eggmanland reality where Eggman has shattered into four different personas, Sonic now goes on a new quest an attempt to restore everything back to normal and save his friends to re-discover who he really is and atone for his actions, leading into the events of Sonic Prime.