Angel Island has become a tranquil metropolis, no longer the battleground for conflict between the Dark Legion and the rest of the Echidna people. Knuckles and his girlfriend Julie-Su are paired up, though not civilly married as they think that commitment is more important than ceremony. The two of them also have a daughter named Lara-Su, who is constantly dismayed at her father's refusal to let her become a member of the Brotherhood of Guardians. The Brotherhood continues its vigil over Mobius from hiding, though the group's numbers are somewhat diminished with the death of Knuckles' father Locke and the reduction of Knuckles' grandfather Sabre to a vegetative state. Lien-Da controls the Dark Legion, and has a son by the name of Rutan. Dimitri the Echidna, as a changed man, also lives with the two of them, and believes that Lien-Da should mend her relationship with Julie-Su. The two apparently disagree over a number of subjects, but remain civil.
As for the other Freedom Fighters and the Chaotix, a number of things for them have changed as well. Tails has married Mina Mongoose and has two children who are friends to Manic, while Rotor Walrus has become a lord of the Kingdom of Acorn. No other members of the Freedom Fighters appear, though it can be presumed that they have settled down with families of their own. Espio is currently married and serving as Knuckles' secretary, and has two daughters by the names of Salma and Juanita, though it is known that Salma is involved having a relationship with Rutan. Vector the Crocodile is also married (but his spouse hasn't been mentioned or revealed), and has a son named Argyle.
Unfortunately, this future has a major crisis facing it. Following the celebration of Lara-Su's sixteenth birthday, Sonic's family pays a visit to Angel Island. When Sonic meets with Knuckles, he learns that Mobius faces imminent destruction. Numerous occasions of immense stress on the space time continuim-including Sonic's access of the Cosmic Interstate, his final battle with Robotnik Prime, and his detonation of the Xorda Quantum Dial-the fabric of space and time is in danger of collapsing, which will cause Mobius to explode.
In an attempt to fix the problem, Sonic and Knuckles agree to a truce. Sonic agrees to use the Tachyon Displacement Chamber, a time machine built by Robotnik and kept in storage for years, to travel to the past and collect information so that the problem can be rectified. Before departing, Knuckles tells Lara-Su that she can become a Guardian, and she stows away aboard the transport. Sonic enters the chamber, but something goes wrong and he disappears. Lara-Su vanishes at the same time, and the time line is irrevocably altered...
Possibly as a result of Sonic's journey to the past, Mobius has been changed almost beyond recognition. The planet is now under the control of Shadow the Hedgehog, who has become Sally's husband through some alteration to the past. With the Dark Legion working together with him and Knuckles apparently serving as his enforcer, he has subjugated the planet. The only piece of good news is that the damage to the time space continuum has apparently been repaired, ending any danger of Mobius being destroyed. However, the handful of Mobians who have escaped losing their memories of the original timeline thanks to being near the Tachyon Displacement chamber when it went off or some other means-sans Knuckles and Lien-Da-have been imprisoned by Shadow's orders though Cobar, Lien-Da's chief scientist, has been possibly killed by Shadow since he is the only person besides Rotor, who is imprisoned, trying to save the space time continium.
Returning, Lara-Su finds a world far different from what she left behind. As a result of the alteration, several of her friends don't exist, while her father appears to be a brutal enforcer of Shadow's will and only she and a handful of others remember the original future. Teaming up with Tails, she accompanies him in a search for Sonic, eventually finding him living on the streets of the city of Portal. However, they are then arrested by Knuckles, who then reveals that he was only serving Shadow's will so he could undermine the power-mad Hedgehog from within.
Working together, Lara-Su and the others free Shadow's prisoners and lead a rebellion, with Sonic going to face his old rival. Shadow soundly defeats him, but Lara-Su takes his place and is able to defeat him using Chaos Control. As a result, her father is convinced of her worthiness to be a Guardian. Upon speaking with Sally later, who considers her relationship with Shadow annulled, the two agree to get married, their old love rekindled.