Prologue

A/N: This story is my idea with for how original Archie comics storyline would have continued before it was rebooted but with a few twists. First events from some of the mainline games would be included but with their events altered to fit in (though no one remembers '06 because of time stuff). The two biggest changes are that the events of Colors and Lost World happen together with Zavok forcing the Wisps to take refuge on Mobius and that the events of Mania and Forces would be merged and had a considerable impact on Mobius itself as explained in the prologue. Secondly characters introduced in the post reboot, fleetway and IDW comics also exist here, but the exact implications will be explored both for specific characters and in general as we get further on. With all that said please enjoy.

The story so far…

It was a time of great trial for heroes of Mobius. Princess Sally robotizied, Antione comatose, Bunnie missing, Nicole ostracized from society and almost the entire Echinda race banished to an unknown dimension. With Ixis Naugus in possession of the Republic of Acorn's throne and the Eggman Empire making gains on several fronts, two teams were formed Team Freedom and Team Fighters to set things right. Team Freedom consisting of Rotor, Nicole, Cream, Big, Heavy and Bomb would protect New Mobotropolis while Team Fighters with Sonic, Tails and Amy would try to bring back Princess Sally and aid people in distress.

After weeks of effort and with the help of Silver and the Artic Freedom Fighters, Team Fighters finally managed to capture Mecha Sally only for a second Genesis Wave to take place. When the world returned to normal both Sally and the Death Egg II had vanished. This close failure had Sonic redouble his efforts, but his mission would be waylaid by other threats, the Black Arms invasion, the Shattered World crisis, and liberation of the wisps and their mother from Zavok and his Deadly Six. Not only that Eggman became more cautious with his prize, putting her out in the field less often so it would sometimes be weeks between sightings.

Meanwhile Naugus had to the public taken ill naming Geoffery St. John as his regent. Geoffery himself became a recluse when not directing council matters. Working with Harvey Who, Elias Acorn had planned with the Secret Freedom Fighters to capture the skunk in a quick nighttime coup and force him and by extension Naugus to abdicate. Meanwhile Naugus had been possessing Geoffery in order to stabilize his mutations and maintain control of his divergent personalities. With his grasp on the council getting tenuous Naugus began to investigate ways to take more direct control of the city. Both forces seemed destined to clash but Eggman had other plans.

By the year 3238 the mad scientist had discovered a gemstone with the power to turn illusions into reality and create a super form for those it was used on. Called the Phantom Ruby Eggman managed to create two synthetic copies, one he gave to a jackal mercenary who then called himself Infinite, the second he used to replace Mecha Sally's power source transforming her yet again. With not only improved combat but tactical ability the former princess proposed a strategy that used new combat robots dubbed the Hard-Boiled Heavies and brainboxes, devices that would alter the victim's personality into a loyal servant of Eggman Empire to be used to insure the Dark Egg Legion's own loyalty and to recruit others as new soldiers or laborers. In the first attack in the new offensive Infinite had defeated Sonic who the world presumed had died. With fall of Mobius' hero, the Phantom Ruby War had begun.

At first it seemed that the Eggman would have a real fight on his hands. Team Fighters was even stronger after Antione had had recovered from his coma and had finished his physical therapy and Bunnie had just returned from what turned into a long-term intelligence gathering mission in her uncle's DEL chapter. But by using a two-pronged attack on New Mobotropolis and Feral Forest involving cutting the capital's nanites from their power source and using brainboxed infiltrators, including Bunnie, to knockout key targets before the initial charge. The city fell within hours and Freedom HQ was destroyed, of the Secret Freedom Fighters Silver was the only one managed to escape while in Team Freedom, Rotor and Nicole managed to evacuate a few civilians including Sir Charles, Jules Hedgehog, Councilor Hamlin, Mina, Ash, Alexis Acorn, Froggy, and the chao Cheese and Chocola. While Geoffrey St. John and Naugus vanished in the struggle, everyone else in the city was brainboxed before the remnants of Team Fighters even realized there was an attack.

In the twenty-four hours after fall of New Mobotropolis Eggman Empire forces launched coordinated attacks on every Freedom Fighter base after Mecha Sally divulged their locations and probable tactics. The surprise attacks resulted in almost every Freedom Fighter becoming a brainboxed member of the DEL. The notable exception being the Chaotix who, while they lost Angel Island, had prevented the Eggman Empire from gaining control of the Master Emerald, though it came at the cost of Mighty and Ray becoming brainboxed.

GUN initially managed to hold off the Eggman Empire but eventually crumbled before the sheer number of foes of on multiple fronts, Shadow had seemingly defected in the beginning of the war and Omega was badly damaged, forcing Rouge and Hope Kintobor into hiding. A week into the conflict the United Federation was forced to surrender and the other Mobian nations did the same almost immediately. Except for a handful of isolated areas, the Eggman Empire now had effectively controlled the planet. Even a dimensional disturbance which transported the landmasses and people of the Sol Zone into the Prime Zone did little to slow the Hard-Boiled Heavies, the DEL and Infinite, as the newly dubbed Sol Islands were brought to heel but not before Blaze managed to seal her Emeralds before she was brainboxed.

The remaining Freedom Fighters reorganized as The Resistance and managed to save civilians while fighting the empire using hit and run tactics. As the most experienced Knuckles was agreed upon as the de facto leader, Amy Rose stepped up in organizing things and many said the girl had matured considerably in a short amount of time and Tails had been working independently but despite his high performance found he himself torn between the loss of Sonic and his frequent encounters with his brainboxed father.

Six months after the war began the Resistance discovered Sonic was alive and held captive on the Death Egg II in orbit of the planet. While the Resistance led a daring rescue attempt Sonic's planed execution left an opening for him to devise his own escape and in meeting the Resistance not only broke free but working with the rescue team managed to destroy the battle station in the resistance's first true victory.

Sonic's return, in combination of the discovery a month earlier of a means to safely deactivate both Brainboxes and the programing that shackled a Robian's free will, had sparked something in The Resistance. Team Fighters was reformed, though they were now dubbed Team Sonic by the people and added a de-brainboxed Cream and Big. Working with Knuckle's Chaotix, who later included a freed Mighty and Ray, Team Dark after Shadow was proven to be impersonated by one of Infinite's phantoms and Omega was repaired, and Team Future who Silver formed with the liberated Blaze and Marine. In the span of days almost all the territory and more importantly people held by the Eggman Empire was liberated.

With the Hard-Boiled Heavies destroyed one by one they had forced Eggman to his last refuge, the new capital he built over the remains of New Mobotropolis after the Nanites died from lack of power and the new seat of his empire within it the Imperial Tower. Both forces clashed in one final battle, where Sonic fought both the last of the Hard-Boiled Heavies, Heavy King, and Infinite at the Tower. With Infinite nearly absorbed by the original Phantom Ruby Sonic managed to save the Jackal who trying to regain some last shred of honor sacrificed his life to destroy Heavy King before the robot could strike the Hedgehog down. But the original Phantom Ruby remained in Eggman's Death Egg Robot, Sonic and his friends managed to destroy the machine but to everyone's surprise the ejection system inside the mech failed and Doctor Eggman, the blight on the lives of all of Mobius, was killed in the resulting explosion.

Leaderless the Dark Egg Legion offered an unconditional surrender and disbanded on the spot, the Eggman Empire effectively ceased to exist. With a now functioning de-roboticizer completed once again everyone who was transformed was changed back, apart from Jules Hedgehog on whom the process would have been fatal. Those who had been legionized however still had to live with whatever modifications were made to their bodies, but work was done to de-stigmatize those legionized, in part by using new tech in the medical field like synth-skin to allow those who wished it to take a more normal appearance.

The capital was taken by the Acorn Republic and rechristened Freedom City and the formerly conquered national governments were reestablished. It was recognized that the old Mobian species conflicts of the past was a factor in Eggman being able to keep his empire after the Bem first granted robotization immunity so a Mobian Accord was agreed upon that would work to promote the interspecies co-operation the Acorn Kingdom was founded upon. The Accord, in conjunction with the United Federation and a now multi species GUN, seemed to make lasting world peace a reality at last.

But to Sonic it was still an incomplete victory, despite everything Mecha Sally managed to escape with the still brainboxed Antione and Bunnie D'coolette-Rabbot in tow. Now weeks later with restoration well underway, it seemed like Team Sonic were the only ones who still hadn't completed their original mission. Not only that Sonic has been having dreams of two different versions of Mobius from the one he knew and he is starting to wonder what these dreams mean…