The first two parts of "The Sonic Terminator" are preoccupied with a largely unrelated opening act which follows-up from the preceding Sonic tale, Pirates of the Mystic Cave.
The Freedom Fighters attack one of Robotnik's airships, commanded by Trusk, which is herding up Emerald Hill folk for transportation to the Veg-o-Fortress on Mount Mobius and conversion into Badniks. However, Sonic appears to have launched on an ill-judged venture this time, because he (and the rest of the Freedom Fighters following him) surrender after being surrounded by Troopers.Sonic seems oddly unperturbed by his plight, though, and indeed his capture is revealed to be part of a greater plan - it was a deliberate ploy to get him on board the airship and leave him better-positioned to inflict damage on the inside while Trusk's vessel is simultaeneously attacked by Captain Plunder and the Sky Pirates. Sonic and the pirates are co-operating following the truce they agreed upon in the previous story, and together they quickly overwhelm the ship, capture Trusk and free the imprisoned Mobians. Strangely, though, the pirates don't remain behind to loot the airship and instead take off at maximum speed - a puzzled Sonic discovers why when Porker Lewis admits that he inadvertantely let slip the location of the Chaos Emeralds to the pirate ghost Filch. The Freedom Fighters pursue the Sky Pirates to the North Cave, but Sonic is forced to give up the Emeralds to Plunder when Tails is captured in the ensuing fight. The dynamic duo immediately set off in pursuit of the Sky Pirates, and Sonic has little difficulty in recovering the Emeralds - in the absence of the cool conditions of the North Cave, the Emeralds became unstable, and absorbed the evil lurking in the pirates (recalling Doctor Kintobor's use of the Emeralds in the Retro-Orbital Chaos Compressor). This temporarily transformed the Sky Pirates into docile, tambourine-tapping hippies! This quirky and unusual adventure serves as a stark and discomfiting contrast to much more forbidding and ominous events happening elsewhere, through, as the newly-unleashed Metallix begins devastating villages, searching for Sonic.
Unaware of what is transpiring, the Freedom Fighters retire to Kintobor's Laboratory. However, while on an errand elsewhere, Amy Rose is captured by Metallix and held at Never Lake as bait to attract Sonic for a confrontation between hedgehog and machine. Sonic immediately runs to Never Lake, and is quite perturbed to see the changes wrought in the landscape - what was formally a heavy forest has now been stripped down into bare grassland. Worse yet, this swept-clean terrain means that there is no way to conceal or disguise the appalling sight of the Miracle Planet. It was formerly an unspoilt jewel in the firmament - now, through Robotnik's diabolical science, it has been degenerated into a machinery-choked flame-spewing figure of Hell.
Amy is trapped atop a tall finger of rock - while Sonic is rescuing her, Metallix confronts him. A protracted and difficult fight ensues - Metallix is no mere badnik and Sonic genuinely has trouble battling him. Eventually Metallix recaptures Amy and retreats to the Miracle Planet, travelling up the magical chain which now binds the world to Mobius. Sonic is not altogether exhilarated at the prospect of rescuing the irritating Amy, but sets off to recover her anyway.
Sonic is disgusted at the transformed Miracle Planet - not an inch of greenery is visible and the entire surface is choked under foul, oily industrial steel and machinery. He collides with Metallix again, but this time his foe proves much more difficult to defeat - he derived from the same machine which overran the Miracle Planet and so can draw upon the limitless power of the entire world. Timely intervention arrives, however, in the shape of a blistering attack from... another Sonic?The interloper seems exactly like Sonic, although this one is pygmy-sized. He Brushes off Sonic's questions and brusquely shoves him into a nearby (and rather conveniently-placed) beam which shrinks Sonic down to the same size of the new figure. Sonic finds himself handed a Time Stone and told to run as Metallix launches another attack on the newcomer. Not knowing what else to do, Sonic obeys, and discovers that his speed activates the Time Stone's power, transporting him back to the Miracle Planet before Robotnik's technology ran rampant over it (at which point the Time Stone vanishes). Discovering the machine which initiated the calamitous corruption of the formerly-pristine world, Sonic launches himself inside (his reduced size giving him the ability to negotiate its confined interior), and rediscovers the Time Stone inside. Sonic removes the Stone, destroying the machine, and his speed brings him back to the present - at which point he realises that the second Sonic he met earlier was, well, himself!
Quickly running through his memory of the encounter to set up his past self on the correct path to bring him back here, Sonic is left to confront Metallix. It looks ominous as Metallix conjures up lightning - but then the blasts sputter, and all of the blighted and rancid machinery - even Metallix himself! - literally fades out as if it never was. Sonic destroyed the machine which polluted the Miracle Planet in the past - so it never grew to cover the world, and the Metallix was never built in the first place.
The Miracle Planet is restored to its natural, immaculate self, but it is no longer deserted... unfortunately. Sonic has been on the Miracle Planet for too long - Mobius has faded from view, and now he has to survive an entire month of Amy's onerous ministrations...!
- The Marxio Brothers are referenced in their capacity as Mario parodies - in Part Three, Sonic complains about the underwhelming experience of playing as the three "electricians" in a Marxio Brothers videogame, while the game screen includes a large pipe (a classic feature of Mario games) and a rendition of a "Bullet Bill" enemy.
- This story opens with a misleading scene of Sonic's apparent death, eventually revealed to be just a test run - the same concept would be reprised in the 'imaginary story' of Day of the Death Egg, and the Sonic the Comic Online story Robotnik Forever!.
- Frustrated with her recapture by Metallix, and maybe recalling recent events in Girl Trouble, Sonic decries Amy as a "professional hostage". He would later transfer this jibe to the increasingly timid Porker Lewis.
- The magical chain which serves as a bridge between Mobius and the Miracle Planet, and the sculptures of Robotnik to which each end is anchored, do not fade with the rest of the Doctor's machinery - while this is primarily a necessary narrative concession so as to give Sonic and Amy a way to actually return home, it can be explained consistently within the narrative by saying that the chain was a creation that was separate from the world-eating machine. How Robotnik created the chain, or obtained a Time Stone, have not to date been explained.
"The Sonic Terminator" does not only follow subsequently from, but directly references the previous story Pirates of the Mystic Cave - it is thus one of the earliest strips to make full and proper use of continuity. The next Sonic story was The Sentinel.