When Scourge was delivered to No-Zone the Zone Cops followed their normal protocol of administering a full medical examination of their patient. Dr. Zuack, No-Zone's resident doctor, discovered that Scourge's recent exposure to Chaos Energy caused the advance of a deadly disease he contracted years ago. The disease was considered incurable by No-Zone's medical staff. Scourge's court appointed lawyers successfully used his illness as reason to overlook the tyrannical hedgehog's crimes and allow him a few more months of freedom. The Zone Cops agreed to let Scourge live out the rest of his natural life out of prison under the condition that he not return to Moebius. Scourge agreed to those terms and asked to be returned to Mobius Prime instead; a request that was granted.

Scourge's first order of business was to find an old business partner of his, Dr. Finitevus, with hope that the doctor could expand his lifespand. Finitevus knew that the disease Scourge contracted was incurable but manipulated Scourge anyway for his own designs. Dr. Finitevus pressured Scourge to do his dirty work gathering intelligence about the city of New Mobotropolis in exchange for a nonexistent cure for his aliment. His initial duties involved sneaking into Mobotropolis to gather sensitive information about the Freedom Fighters for his personal project such as their height, weight, and any unusual quirks. The results of this research was later taken for " evidence " by Shadow the Hedgehog.

A few days later Sally led the Freedom Fighters to Freedom HQ where they captured Scourge with relative ease. Scourge, beginning to doubt Dr. Finitevus, allowed himself to be captured believing that the Freedom Fighters would be able to diagnose and cure his increasingly more obvious illness. Before vital clues could be transported to Dr. Quack for analysis Princess Sally was kidnapped, captured, and temporarily controlled by Dr. Finitevus. Around the same time Sonic accidentally knocked over an ancient urn contained a sealed Demigod named Mephiles while waiting for Sally. Mephiles took a form resembling Sonic for his own personal gains before leaving in search of Chaos Emeralds.

Sally inhibited strange behavior upon returning to the other Freedom Fighters. When this ultimately led her to hand the Kingdom's Chaos Emerald over to Mephiles Sonic, Bunnie, and Antoine called an intervention to try to subdue the Princess. Antoine brought Sally to Dr. Quack who in turn tranquilized her. Dr. Quack was unfortunately captured before he can properly diagnose Sally. Under Finitevus' command Dr. Quack began poisoning Sally with lethal doses of anesthesia and giving incorrect diagnoses to her friends and family to cover his tracks. This plot was put to an end by Shadow the Hedgehog's inquisitive questions. When inconsistencies arose behind Quack's behavior Finitevus ordered him to move Sally into an Operating Room where he and his hospital staff were executed. The Freedom Fighters managed to save Sally before she too perished.

Concerned that their investigation into Mephiles and Scourge had been compromised the Freedom Fighters tried to band together during a time where a large number of citizens in Mobotropolis were vanishing. Sonic was temporarily among them when he was abducted by Mephiles and sent into the far future. There he learned a little about the history of Mephiles, met a much older Shadow, and fought off the temptations of Mephiles to return to his own time. A soft spoken young hedgehog boy named Silver and his guardian, Princess Blaze, enter Mobotropolis around the time of Sonic's return claiming to have the secret to defeating Mephiles. They presented two Moon Stones with enough power to temporarily weaken Mephiles.

While Shadow made an attempt to regroup the Freedom Fighters Scourge was brought to Mobotropolis' hospital to undergo medical observation following a medical episode. Instead of finding a regular staff doctor the group found Dr. Finitevus who offered his services in watching over Scourge and other injured mobians, pointing out that the hospital was understaffed. The Freedom Fighters were unwilling to trust another villain after one of their own turned sinister and refused to hand over Scourge leading Finitevus to attempt to kidnap the weakened hedgehog. A bloody battle ensured when Bunnie pursued Scourge and Dr. Finitevus through a Warp Ring. Bunnie managed to throw Scourge to safety back in Mobotropolis but was cut off by Finitevus before she could escape. Scourge in turn assisted in rescuing Bunnie by leading Sonic and Shadow to Finitevus' domain so she could be rescued before Finitevus finished her off.

Once the group was safely back in Mobotropolis Bunnie's was treated and Scourge was taken back to the jail for an interrogation. At the jail Scourge revealed what he knew about Dr. Finitevus' plans. He kidnapped the majority of Mobotropolis' citizens for genetic screening in hopes of finding suitable mates for the declining population of echindas in Albion. Those that made the cut were supposed to be held over for breeding but he was largely unhappy with the " samples " he took from Mobotropolis. Scourge agreed to go on a search and rescue mission to Finitevus' domain with Sonic, Shadow, and Knuckles while the other Freedom Fighters gathered up the remaining citizens of Mobotropolis to protect them in an isolated area. As the group started to move Sally the princess awoke from her drug induced coma feeling much like her old self.

The mission to Finitevus' domain ultimately proved to be bittersweet. While the group failed to find any mobians to rescue before being forced to retreat they did manage to steal a Hexed Chaos Emerald. The emerald and Scourge were seized within minutes by Mephiles. Mephiles took the emerald into his growing collection and handed the hedgehog over to Finitevus since he had no further use for him. Finitevus also thought that Scourge reached the extent of his usefulness in his plans and decided to torture him with the help of his long term business partner; Kommisar Lien-da. Shortly after being thrown out of the domain near Mobotropolis Scourge succumbed to his illness and died ... just as Sonic and Shadow began their next mission.

Sonic and Shadow moved into Casinopolis to retrieve a Chaos Emerald from Master Mongul's possession. The Emerald proved to be an easy one to retrieve since Mongul left it in the protection of one of his employees, Bean, while he went to The United Federation to run an errand. Bean gave them the Emerald under the condition that he be offered protection from a soon to be angry Mongol by the Freedom Fighters. It was a term that they complied with ... for now.

Bean was transported to a temporary prison cell with the rest of the protected mobians for his own safety upon returning to Mobotropolis. As the Freedom Fighters tried to round up a few missing in action stragglers to move into the Civic Center with the others they came across Scourge's body. Sonic volunteered to move Scourge into the hospital's morgue. Just as he moved to leave an angry and bloodied Kommisar came onto the scene claiming Dr. Finitevus turned against her. The wounded Legionnaire eventually agreed to an interrogation but would only speak to Sonic. The others were asked to wait outside while Sonic attended to her wounds.

Around the same time a mysterious mobian named Shade honed in on a Chaos Emerald in Rouge's hold back in Mobotropolis. The resulting fight lead to the attacker, Shade, Rouge, and Mighty being transported to a place called the Twlight Cage. Rouge's Emerald ultimately landed in the hands of the Nocturne's ruler, Imperator Ix, who intended on using the Emerald to return his exiled people to Mobius for some long desired revenge.

Kommisar explained that what Scourge told them earlier was originally true but Finitevus' plans changed since then. Finitevus couldn't find any acceptable samples to breed and simply executed the mobians from Mobotropolis. She herself was deemed inadequate for the breeding program and just barely managed to escape with her life. Kommisar confirmed that Finitevus was finished kidnapping mobians from Mobotropolis and set his sights on the neighboring Kingdom of Merica. She offers to assist the Freedom Fighters in saving the kidnapped Mercians before their execution in hopes of saving herself further embarrassment.

This time Sonic, Shadow, Silver, Rob, Sally, Bunnie, and Kommisar went into Dr. Finitevus' domain with the positions of the held prisoners. While prisoners in Sonic's, Shadow's, and Bunnie's quadrants were safe Rob stumbled upon a massacre in progress in his quadrant. Rob's appearance in the fray alerted Finitevus to intruders. He sent out a remote signal to take violent control of mobians in Sally's quadrant which ultimately overwhelmed her. The mobians in the other quadrants were beyond his realm of control thanks to a device planted by NICOLE. A bloody battle insured between Rob and Dr. Finitevus. In the end Rob managed to force Finitevus into a retreat though not before the majority of the mobians in the quadrant including members of his own family were slaughtered.

Rob returned the others to Mobotropolis where two of the three other groups were waiting for him. They returned on the tail end of an opportunist attack by Dr. Eggman and his employee, Nack, put to an end by Knuckles.

Sonic was also going to go meet the group when he was intercepted by a battle weary Dr. Finitevus. Though exhausted from his battle with Rob he managed to ambush Sonic and pressure him into giving up his Chaos Emeralds. The hedgehog was returned to Mobotropolis after their transaction so Finitevus could prepare the Emeralds for Mephiles' arrival. There Nack the Weasel tried to take advantage of Sonic's weakened state only to be (easily) stopped by Shadow.

Mephiles returned to Mobius after successful negotiations with Imperator Ix for his Chaos Emerald. That one combined with his and Finitevus' stashes gave him enough power to draw Ilbis out of its living vessel, Silver, to form Solaris. Solaris began destroying the very fabric of reality immediately. To preserve their existence Sonic, Shadow, Knuckles, Blaze, and Silver shared the remaining power in the Chaos Emeralds to achieve their Super Forms in hopes of defeating the God.

Just as it seems they've made progress something odd happens ...