It is another idyllic day in Green Zone. A blue streak in red sneakers sears across the tops of checkerboard hills and bridges - why, it's none other than the speedster Sonic as he rushes through loop-de-loops and bounces from suspended platforms, accompanied by his constant companion, Tails. Palm trees dance, the grass grows rhythmic in mower-stripe patterns, and blue sea reflects the blue sky.
There are no enemies, there are no threats. Sonic's speed and bounds are unparalleled, his rolls sending him through tubes with "little brother" Tails barely able to keep up.
But, no paradise can remain unstained forever. For even in this Eden, there is always decay. Eggman is growing. From the shadows behind un-collected coins and ignored platforms, minuscule round men with moustaches and beak-noses bubble forth, pixel by pixel, from black glitch-pools.
At first, the Eggmen are so small that they might be mistaken for lines of ants or clouds of gnats, but as Sonic runs, so too do the now-more-frequent pools churn upwards larger Eggmen, some almost as large as Sonic himself. Though the smaller enemies elude any attack, Sonic still shows off his prowess in the destruction of as many larger Eggmen that he can. The defeated ones burst open, metallic and hollow inside, devoid of a need for their former animal core.
Despite their teeming number, the Eggmen as a whole ignore Sonic, the majority of them scurrying between the palm trees, ducking under stones, or slipping behind the platforms and bridges to hide their presence as the mass travels forward. Sonic runs alongside them until he makes it to the end of the zone, where a huge wall divides Green Zone from the next region. In this threshold, the sky looms an industrial orange. We see in the wall all the parts from Eggman's past machines, as well the crack through which the Eggmen funnel themselves.
Panels in the ground open up with a rumbling groan, and the zone's Boss emerges; a humanoid Eggman, who, though 1.5 times larger than his former size, looks quite similar to our old enemy. He pilots a robotic car. Its carriage is Eggman's head. Each one of Sonic's attacks break the Eggman Rider down into smaller and smaller Eggmen, that, too, seep like water through crevices in the wall. But then, Sonic strikes a spin attack upon the Eggman's core – the Eggman Rider explodes, and in doing so, blasts a hole in the wall.
From the robo-car's wreckage, the first chaos emerald rises and glows. Sonic collects the coveted green gem, then runs through the now burst-open wall into the next zone.
Sonic follows a passage that leads underground, into the Toy Factory Zone. Inside the halls of this industrial playroom, Sonic catapults into and out of gashapon machines, rides atop toy trains, and careens through stacks of blocks, while avoiding the pistons and crunching gears. This is no whimsical exploration, however, for this factory has now been co-opted by the Eggmen, who pull the levers and push the glowing buttons, the machines of the assembly line producing larger and more complex Eggmen than ever before.
These Eggmen, more powerful than those in Green Zone, attack Sonic with their robo-fists and rockets. A sandy black river runs along the lowest level of the factory, its oily waters carrying off the shells of dead Eggmen, defective models, broken parts, and other by-products of industry. The muck seeps down into grates.
Sonic reaches a large chamber at the end of the level, and fights the boss of the level - Toy Eggman, who resembles a blocky, giant toy robot. Other, thin Eggmen watch from the sidelines, but scatter like mice into the shadows once the boss is defeated. Its eradication leaves behind the second chaos emerald. Sonic gathers the gem, which is yellow, and has a wind-up key in its side. Our hero then presses a red button at the end of the room, which starts the self-destruction sequence for the factory. He and Tails only narrowly escape the explosion and flee into the next zone.
...but, the world beyond the factory is not the reprieve that we could have been led to believe. The sky is sunless, all plants either dying or already dead, the soil tainted by the factory’s black river, and the air made hazy by the smokestack’s acid reflux exhaust. Dead Eggmen litter the area in piles, with some of these corpse-heap mounds and gigantic shells being large enough to go inside. Though Sonic's path is blocked by a few grey, corrupted hangers-on who still attempt to rejoin the greater Eggman swarm, this dismal area is all but abandoned. Incinerators below the ground burn both the corpses and imperfect survivors.
Within this bleak place, Sonic crosses through a few brief patches of land which shimmer with color and light - but each oasis is revealed by Sonic’s passage-through to be nothing more than a flickering projection. Whether these hologram machines either discarded parts of a larger construction, or placed here deliberately to mislead our hero, they are now unable to hide the world’s true nature. Has this gone on for longer than Sonic imagined? Was even Green Zone’s paradise a similar projection?
Sonic reaches the end of Depleted Dream Zone, and stands on a cliff edge that overlooks a glowing neon Eggman city. The boss then appears, and atop this precipice, Sonic fights the huge, deformed, Reject Eggman - though Sonic is successful in both defeating it and recovering the black, coal-like third chaos emerald within), the beast, in its death throes, shoots Sonic through the head with a beam of light. The screen goes white.
After a brief kaleidoscopic abstraction that fills the screen, Sonic reawakens. This world is simple, abstract. There are no plants, but instead, platforms and structures are constructed out of geometric shapes that float above an endless pearlescent ocean. As Sonic destroys various obstacles, we see that there are Eggmen hiding underneath, but they flee from view as soon as they are revealed - Sonic is unable to kill even a single one. An undulating shape floats in the sky, though its borders are blurry, indistinct.
Gradually, the shapes upon which Sonic runs grow less and less abstract, the colors more uniform shades of blue and tan. We see now that Sonic is running on deformed, bizarre versions of himself - he races up ramps in the shape of his spines, and does spin-dashes beneath looping columns of arms and legs. In addition, the shape in the background continues to stir, and with each undulation, it more and more resembles an embryonic Sonic; enormous, dormant.
Finally, Sonic approaches a mirror at the edge of this zone. In it, he sees his own reflection, which emerges and attacks him. A boss battle with this Duplicate Sonic now takes place, with the "true" Sonic of course proving victorious. As the false Sonic falls, however, the truth is revealed; he was just another Eggman after all. This Eggman drops the fourth chaos emerald, which looks like Sonic compressed in simple geometric form.
With this, the world fades white and dissolves.
Sonic awakens inside a dark chamber deep within the Censored Signal Zone, the stronghold metropolis of the now innummerable Eggmen. This windowless machine is filled with seething tangles of black wires, circuit boards, control panels, and screens. Tails nudges at Sonic’s side, and our hero finally rises to his feet.
Sonic runs along the route that cuts through the innermost part of eggman city. The Eggmen here are myriad, teeming and moving in channels, but in their element, they seem unconcerned with Sonic himself. A great many of them stare at the emormous displays that dominate the sides of buildings, upon which play familiar scenes, depicting sequences from earlier games, in addition to non-existent pieces of Sonic media.
Sonic reaches the uppermost section of the zone, and enters a control room walled with many more screens. From these screens, the imposing holographic Eggmen Centurions emerge. Sonic fights them, and the televisions continue to flash disorienting images, making the Eggmen themselves hard to discern. Sonic nonetheless defeats these Eggmen, the last of which drops the fifth chaos emerald, seems as flat and holographic as the Eggmen had been.
The next room contains a device which looks like a transporter. Sonic steps upon the center of the machine, but then, the walls begin to rumble, and Eggmen flood outwards, the swarm so great that they are more like a liquid than anything else. Tails, who had accompanied our hero so tirelessly, cannot hold them off, and is killed by the tearing, ravenous robo-hands, though not before activating the teleporter.
Left with no time to grieve or retrieve his friend’s body, Sonic is beamed away just as these Eggmen envelop the machine's launch pad.
The beam transports Sonic onto the Forgotten Moon Zone. This zone is grey, quiet, all but lifeless save for a few dust-colored tendrils that grow from beneath certain cracked murals. These murals depict a history long since forgotten on the surface of the planet, and on the walls and pillars of the zone's ancient palace we see stylized animals, much like Sonic and his ilk. Eggman does not exist in this world, for even via such iconic depictions, it can be inferred that perpetuating his image would only perpetuate his power.
Sonic travels deeper and deeper into this lostland. We can see our former planet in the sky above. It has been overtaken by Eggman, his face now visible in the layout of cities and other structures large enough to be seen from space. What little green remains is riddled with holes of black, red, and yellow.
At last, Sonic reaches his destination, a room lined with multi-colored murals more complex than those we have seen thus far. The sixth chaos emerald sits in the center of a large chamber, its appearance crystalline and solid red. But before Sonic can reach it, a crimson shape moves in from the sides - it is Knuckles, who stands guard before this most precious artifact. Sonic must do battle, and the sort of dance they play mirrors the fight Sonic had with his duplicate fake self earlier. But, this time, Sonic holds back - he shows Knuckles mercy where he had none on his own copycat. Knuckles bows to Sonic’s power and relinquishes the sixth chaos emerald.
Sonic returns to the transporter, waving goodbye to Knuckles as light fills the screen again.
Sonic stands upon the planet's surface once again. This time, however, there is no more city - the structure that Sonic travels through is, in fact, a giant Eggman whose body encompasses the entirety of the planet. Trapped inside this colossus, Sonic rushes through Eggman’s heart, veins, lungs, and intestines, sharing this space with throngs of fanciful Eggmen too numerous to count. (Parasites, or citizens?)
Sonic reaches Eggman’s center, and fights the Matryoshka Eggman and its nesting dolls. Each Eggman he fells cracks open to reveal a new enemy, and the series would seem to continue inward forever. Sonic will not be defeated, however, and destroys the ground upon which the Eggman stands, sending it careening downwards into the black oil beneath. From the sludges, the final chaos emerald rises, crystalline and Eggman-shaped. Sonic hesitates for only a moment before he gathers it up.
Sonic now embraces the power of the chaos emeralds. A glowing light overtakes the screen, and we now see the giant Sonic embryo from the skies of the Ego Delusiac Zone - but it is now mature, and its form becomes that of Supersonic. It is this projection, so enormous that it, too, must be visible from space. In a glorious battle, Sonic's gleaming avatar fights the Eggman that, if allowed, would otherwise become the size of the known universe.
At last, the unbounded hero is victorious in his apocalyptic assault, and the Eggman melts and evaporates away just as the Supersonic projection collapses onto the ocean below. As the massive hedgehog body falls, it dissipates to nothing, and leaves no impact. In the afterglow of this cataclysmic battle, the still flesh-and-blood Sonic lays, exhausted, overlooking the new world. And, Sonic's player might clutch their face in disbelief - for this quiet earth so resembles the pearlescent sea from Sonic's visions in the Ego Delusiac Zone. Will Sonic, much like Eggman had done before, attempt to remake the world in his own image?
From the floating island on which Sonic stands, our hero watches as the tides roil and lands grow upwards from the sea. There are no longer any forests, but there are now seeds.
Knuckles gazes on from his refuge on the moon.
As the credits roll, we see the forest, which spreads out over the land once more.