[2][3] The series features a cast of hundreds of characters, consisting of both those derived from the Sonic games and those original to the comics, with stories focused on a crime-fighting organization called the Freedom Fighters, led by Sonic, as they face off against series antagonist Doctor Eggman alongside a variety of other villains.

While the series largely consists of its own continuity, certain issues implemented aspects of the Sonic video games into their plots and settings.

[10] The comics follow the adventures of Sonic the Hedgehog and his friends, called the Freedom Fighters, who battle against the evil Doctor Robotnik.

The original universe, which remained canon until the comic's 247th issue, is set on the planet Mobius, an alternate version of Earth where animals were mutated into the anthropomorphic Mobians.

The Xorda, an extraterrestrial race whose past actions led to the creation of Mobius and evolved anthropomorphic animals, try to destroy the planet.

Sally's father, King Maximillian, is poisoned by Antoine's evil counterpart, Patch, and hands the throne over to his son Prince Elias.

Tails’ father Amadeus tries to bring democracy to the city against the monarchy, Sally preventing a civil war by establishing the Council of Acorn, consisting of royal and public officials.

Eggman suffers a massive mental breakdown due to Sonic foiling his plans for world domination one too many times and is temporarily institutionalized, allowing Snively and the Iron Queen, Regina Ferrum, to take over his empire in the interim, leading to a lengthy war against the Freedom Fighters.

In the new continuity, Sonic and Dr. Eggman retain their memories of everything they both knew before the Super Genesis Wave, which are later restored onto Nagus, Tails, Rotor, Antoine, Bunnie, Sally and Amy when they make contact with Nicole.

The comic also introduces Naugus' sister Wendy, a witch who pledges allegiance to Eggman and plots to gain the Cacophonic Conch.

The Sonic Boom line began in October 2014, and was later incorporated into Worlds Unite before concluding with its eleventh issue in September 2015.

The comic book has had a large cast of characters, primarily originating from the video games, the 1993 animated series, and other media.

A number of characters were created by various writers including Ken Penders, Ian Flynn, Michael Gallagher, Karl Bollers, Scott Fulop, and Dan Slott.

After briefly discussing the series' concept and that the 4-issue miniseries would have 3 self-contained stories in each issue, Gallagher was told by Edelman to "establish the characters quickly through strong exposition" using "visuals from the game" (which would be faxed to him) and needed the first script in a week.

[129][130] Penders planned on continuing his "Mobius 25 Years Later" story independently, and declared that everything using his copyrighted works since issue #159 of the main comic[a] was "essentially unauthorised".

He had been prompted to do so after fans contacted him asking if he had anything to do with the release of Sonic Chronicles: The Dark Brotherhood, which he did not;[129] Penders believed the game used concepts and characters similar to those he had written for the comic series.

[133] However, Archie were unable to produce the original copy of their contract with Penders, nor those of any other artist who had ever worked on Sonic, opening them for future lawsuits.

[134][130] He would later turn the "Mobius 25 Years Later" continuation project into The Lara Su Chronicles;[135] Archie would initially write his characters out of future comics, rewriting issues mid-lawsuit to remove any references to them and not republishing stories involving them, before rebooting the canon entirely to retcon out not only his but any other former writers' original characters and concepts fully.

[137] He cited the Penders case as justification for his claims, and gave nearly a thousand examples of times Archie had allegedly wrongly used his characters or reprinted stories involving them.

Destructoid praised the comic series, especially the earlier issues during the 1990s, for adding more backstory and character interaction than was presented in the Sonic video games for the Sega Genesis.