The series follows a unique format, in which its lead character and story arc change every four issues, and usually occur concurrently with those in the flagship Sonic title, though within different locations.

In this arc, time-traveler Silver the Hedgehog travels to this time period in an attempt to thwart events that will bring devastation to the future from which he hails.

In the process, he ends up joining forces with a new team of Freedom Fighters, made up of children of the heroes from the present reality of the series, to thwart the evil King Shadow the Hedgehog, who unleashes a monstrous fusion of Tikal and Chaos from the video game Sonic Adventure.

As a result of the search, they end up fighting Dr. Finitevus and his temporary allies, a chapter of the Dark Egg Legion composed almost entirely of Platypus members, led by Grandmaster Bill, a former Freedom Fighter.

This arc also introduced Thrash the Tasmanian Devil as a temporary Freedom Fighter member, but who acts recklessly and shows particular animosity towards echidnas.

In the comic's version of events, Antoine and Bunnie D'Coolette, Tails' fellow Freedom Fighters, joined him on this adventure, having traveled with him to Cocoa Island for an overdue honeymoon.

Together, this group fought against the villainous Enerjak and his minions, who consisted of robotic slaves created from the stolen life force of various characters previously introduced in the series.

Having previously been handed over to an inter-dimensional police force known as the Zone Cops, Scourge had lost much of his confidence and become the punching bag of many of his fellow inmates.

In this way the arc adapts concepts from the video game Sonic Riders, though again with elements from the ongoing comic series playing a heavy role.

This was one of the few arcs to feature Sonic with some prominence, as the Armada eventually attacked the Freedom Fighters' home city in search of their homeland.

In doing so, the group operated in disguise and using codenames so as to prevent their true identities from being discovered by Naugus, who would hurt their vulnerable families and friends if found out.

Issues #51–54 were included in Archie's "Worlds Collide" story arc, a twelve-issue event featuring a crossover between the Sonic the Hedgehog and Mega Man comic series produced by the company.

Amy Rose and Cream the Rabbit, along with recurring anti-villains Bark the Polar Bear and Bean the Dynamite, are transported to the Sol Dimension, the world of Blaze the Cat.

Issues #63–66 encompass the "Great Chaos Caper," which runs parallel to the Sonic Unleashed adaptation taking place in the main series.

In this, Knuckles and the Chaotix join forces in the hunt for Chaos Emeralds to help the Freedom Fighters in the quest to restore the world to normal after its shattering.

In the process, they must contend with the minions of Dark Gaia and the Hooligans, a team of classic Sonic game villains consisting of Nack the Weasel, Bark the Polar Bear, and Bean the Dynamite.

Their infighting results in Eclipse taking the Emerald, forcing Knuckles to shatter it and thus leading to his involvement in the main series' storyline.

Taking place in a both the "Digital World" and on Isolated Island (from the game Knuckles Chaotix), it introduces the malevolent computer program Phage and Nicole's creator in the new reality, Dr. Ellidy.

Helping him on his mission are scientist Professor Von Schlemmer (a character from Adventures of Sonic the Hedgehog) and Gold the Tenrec; opposing them is the evil Onyx City Council and their force of Civil Protection Robots.