Several years have passed, and an older Chris prepares to make a surprise visitation to Sonic's world using a reconstructed gateway. Meanwhile, Sonic's world is attacked by an invasion force from the stars, planet consumers known as The Metarex. Sonic and his friends meet a victim of their wrath named Cosmo, who alerts the Hedgehog of the threat at hand
Sonic's team decide to help Cosmo liberate the remaining planets from the Metarex's vicious attacks, and also to seek out the cosmos scattered Chaos Emeralds., Tails develops a new spaceship, powered by the Master Emerald, but a Metarex agent arrives to eliminate them before they can even begin
Arriving on a world submerged in water, Sonic faces his most dangerous environment yet, and Chris faces a personal crisis when he realizes the limits of being a human after he fails to prevent Sonic from falling into the hands of the Metarex
Eggman manipulates Knuckles into giving the recently acquired Chaos Emerald to him, but Sonic refuses, pitting the two rivals against one another once again, putting Cosmo in danger when Eggman seizes her to use as a hostage
On an Ice world, Sonic and the team locate a Chaos Emerald trapped in ice, and face a Metarex who can absorb it's energy
With Sonic missing on a planet filled with plant life, Amy, Cream, and Cosmo embark on their own search and rescue mission, and come across a dangerous Metarex. Meanwhile,. Sonic is eventually discovered by Knuckles, but both are confronted by Eggman
The Chaotix crew are assigned a new mission by Cream;'s mother to find her and confirm her present condition. Communicating with Earth, they acquire a new spacecraft and pursue Sonic's ship into the depths of space, but misunderstandings between the two crews turn to heated conflict
Sonic's team are drawn into a Metarex ambush and are overpowered, but the arrival of an old rival long thought dead turns the tide in their favor.
A powerful Metarex warship familiar to Cosmo engages in a brual confrontation with the Blue Tornado, Sonic and Shadow decide to brave the danger within the warship to knock it out of commision
Separated from their friends, Tails and Cosmo brave a Metarex factory in an effort to locate another Chaos Emerald
In order to acquire the final two Chaos Emeralds, Sonic and Eggman's forces must join together. After successfully infiltrating the Metarex factory housing the Emeralds, Sonic soon comes face to face with the commanding force behind the Metarex armies, Dark Oak.
Dark Oak turns out to be a hologram, leaving Sonic without an opportunity to eliminate him, and trapping him in a factory marked for destruction by a vast Metarex fleet outside. Chris manages to infiltrate Eggman's vessel in an effort to seize the Chaos Emeralds, but is stopped by Shadow, resulting in all seven Emeralds being brought together, transforming Sonic and Shadow into their more powerful forms
Cosmo throws a party to relieve Chaotix and Sonic's crew of their stress from recent Metarex conflict, whilst Chaotix attempt to aid Tails in capturing Cosmo's heart
Sonic and the Typhoon slowly approach the Metarex homeworld, as they confront the malevolent and powerful Zelkova
Sonics journey into the Metarex home world leads to two of his closest friends being captured by the Metarex, which begins a slow descent in his mind, unleashing a dormant and brutal dark gene that transforms him into an unrelenting, merciless being who can only be salvaged by Eggman
Shadow and Rouge assist a group of freedom fighters on a planet locked in battle against the Metarex in locating a Chaos Emerald to aid them, joining them is resistance fighter Molly, who sees Shadow as the "Black Wind" of her planet's legends who will deliver them. It's not long before treachery and greater stakes unfold in the hunt for the Emerald
As the Typhoon's crew help to liberate another world from the Metarex grip, Amy attempts to force Sonic to show her his affections, even resorting to a love spell, but when she springs her trap, she only succeeds in snaring Tails and Cosmo, forcing the two to finally admit their own feelings...
Tails is thrown into the rank of commander when Sonic and Knuckles are injured whilst attempting to divert the Typhoon away from a crushing black hole that also threatens Eggman...
Sonic's crew become stranded on a nightmare world with seemingly no hope of escape, only familiar allies can hope to salvage them
Zelkova's devastating return coincides with Sonics crew finally uncovering the secrets of the Metarex...
Shadow and Rouge return to the Typhoon, seeking the one person on board he believes to be directly responsible for several recent, and more intense, Metarex attacks: Cosmo. As Sonics team battle with Shadow to safeguard their friend, they are soon attacked by Dark Oak, who reveals the shattering truth about Cosmo
Tails and Knuckles clash over how to remove Cosmo's Metarex transmitter without robbing her of vision and hearing, as Cosmo's homeworld reveals to the crew of the Typhoon another startling truth behind the Metarex...
With Eggman now a hostage of The Metarex, the crew of the Typhoon pursue Dark Oak to mysterious coordinates important to him, Sonics team find Dark Oak has assembled all of the seven Chaos Emeralds around a planet of water, holding within it a planet egg. As Oak and his Metarex cohorts use the Emeralds and the egg to mutate into Dragon like forms, Sonic is cast into the depths of the planet...
Sonic remains trapped with the water world as the ascension of Dark Oak continues. The Typhoon crew attempts to cut off his energy by using the Master Emerald and the Sonic Driver, but brief success in this strategy turns to tragedy as the Emerald shatters and the Metarex absorbs all of the Chaos energy. Amy makes a final desperate attempt to retreive Sonic
Dark Oak completes his ascension and begins draining the life force of those who oppose him. Cosmo attempts to flee with the Chaos Emeralds only to be struck down in space, which fortunately provides Sonic and Shadow with the means of becoming super.
But with all of their power, they are unable to defeat Oak totally, leading Cosmo to make a final decision that can only end in death to preserve life...
In the aftermath of Cosmo's death, Tails slowly accepts his loss, flash-backing to the final moments of Dark Oak's defeat and remembering what other sacrifices were made to ensure the survival of the others. Meanwhile, Chris is provided with an opportunity to return home, but it requires making a hasty exit from Mobius, or the chance will be lost.