The story marked the largest collective creative effort ever seen in Sonic the Comic or the online edition, showcasing the talents of four writers and 17 different artists, some new to the comic.
- Ed Reynolds - overall script.
- Jamie J - script on pages 4-5, 8-9 and 19-20.
- Stephen 'Spydaman' Davis - script on pages 6-7 and 17-18, as well as art for pages 13-15.
- Charles Ellis - script on pages 15-16, as well as overall editor.
- Zak Simmonds-Hurn - art on pages 1-3.
- Mike Corker - art on pages 4-5, 16 and 24-25, as well as overall lettering and compiling.
- Saku, Emmy Roll & Lkt (Team Mobius) - art on pages 6-7 and 17-18.
- Adamis - art on pages 8-12 and 15.
- Fast Ashadonic - colouring on pages 8-9.
- Matt Dittmer - art on pages 19-20
- Iain Stewart - colouring on pages 19-20
- Stiv - art on pages 16, 21-23 and 26
- Matthew Allen Smith - inking colouring on page 16
- Bakasam - art on page 15
- Alex Willmore & Lauren Anne Sharp - art on page 15
- Chris G - art on page 16
- Thalia Evans - art on page 16
This special story features (or mentions) no less than 40 characters from the entire history of STC and STC-O. Many are merely one panel cameos, but others play a major part in the story:
- Sonic the Hedgehog
- Bob Beaky (Sonic's disguise)
- "Tom", the rat in charge of the Portal & Gift Store
- Miles "Tails" Prower
- Kintobor Computer
- Knuckles the Echidna
- Mighty the Armadillo
- Espio the Chameleon
- Charmy Bee
- Vector the Crocodile
- Porker Lewis
- Vichama (in thought only)
- Amy Rose
- Johnny Lightfoot (in statue and in name)
- Hobson & Choy
- Big the Cat
- Norris Wimple
- N1G31 and 3150N
- Grimer (mentioned)
- Cedric the Elephant (in Badnik form)
- Metallix (the Knuckles version)
- Doctor Robotnik
- Sally Acorn
- Agiatha Witchbrew
- Ancient Tree
- Grouchio Marxio
- Chicio Marxio
- Sab (background)
- Sol Furic (background)
- The shirtless dog from Casino Night
- Don Long-Legs
- Captain Plunder
- Fabian Vane
- Masad Akaan
- Police Chief Bodger
- Kat Adie (mentioned)
- Shortfuse the Cybernik (mentioned)
As the story represents a worldwide invasion, a multitude of Zones are shown:
- Green Hill Zone
- Emerald Hill Zone
- Floating Island
- Metropolis Zone
- Turquoise Hill Zone
- Metropolis Park
- Chemical Plant Zone
- Coal Creek Zone
- Casino Night Zone
- Scourge Bay
- Hill Top Zone
- Eldorado Zone (mentioned)
The plot follows on from Sonic's fall from grace in the public's eyes. Sonic is about to leave Mobius forever through a dimensional portal when a commotion is heard outside. It isn't long before Sonic sees the skies filled with Badniks, launching an invasion. Ditching his 'Bob Beaky' disguise, Sonic heads into battle.
In the Emerald Hill Zone, Tails is struggling to cope and can't get in contact with anyone else. He makes it back to the Freedom Fighters' base just in time to rescue the Kintobor Computer (now stored on a Ring), before Robotnik's Badniks destroy the base.
On the Floating Island, Knuckles, Tikal, Porker and the Chaotix Crew observe the war from above. Knuckles turns his back on it, returning to the Emerald Chamber to fulfill his duties as guardian, but Mighty and Vector convince him to attack Robotnik before he attacks them. The team head off to man the island's weapons and defences.
In the Metropolis Zone, Amy is shocked to see the return of the Badniks, along with a huge Caterkiller (later dubbed an Uber-Nik). Getting to work destroying the invaders, she is aided by the people of the city, including those who fought alongside her in the STC story, Solidarity. With Amy leading the citizens on, everyone charges at the Badniks.
In another Zone, Sonic proceeds to smash up another horde of Badniks, including many old major threats which are simply brushed aside. The trail of smashed Badniks eventually leads to a new base styled on the head of Robotnik. Inside, Sonic finds the Chaos Tap, now enlarged, and assumes that the Drakon Empire are behind the invasion. Further inside the base, Sonic finds Robotnik strapped into a supercomputer, using his mind to control the invasion. The Drakons plan to seize control of Mobius and make it a principality, with Robotnik as its ruler. However, Robotnik's cameras show several Zones fighting back against the robot threat.
Back on the Floating Island, the Floating Island fires upon Robotnik's warships with the energy sphere last seen in Disaster!. The island continues to show off more weapons such as molten lava from the Lava Reef Zone and Gum Tree Berries once used to attack Vermin the Cybernik.
On the surface of Mobius, Choy is filming all the events, ready to claim his award for his take on events. His companion, Hobson, loses control and attacks Choy for finding the invasion "amusing". He and Amy convince Choy to use his camera to show the world the efforts to tackle the enemy threat, with stories from those affected. Sonic and Robotnik are watching this news story and Sonic is defiant. Unfortunately, Robotnik targets the Emerald Hill Zone and Sonic rushes off to save his home.
In the Emerald Hill Zone, Tails and the Emerald Hill Folk are fighting off Badniks when a huge robot with the face and voice of Robotnik appears. Tails finds it easy to dodge the robot's attacks but can find no way to hurt it. Sonic appears and tells Tails to distract the robot while Sonic jumps inside and dismantles it. The crowd believe that Tails beat it with a single punch and he becomes the hero of the Zone.
The next morning, Sonic meets Tails again and tells him about the Metallix acting as Sonic in the past few months. Tails forgives him and is ready to leave with Sonic when the hedgehog tells him he must fight alone and that Tails must be the new hero of Mobius. Before Tails can object, he receives a new plea for help and Sonic speeds off. With Tails left to fight the new threat, Sonic runs off for the next battle.
Several characters made their debuts in Sonic the Comic Online, such as Fabian Vane, the Flicky, Monkey, the living trees of Metropolis and Sab, amongst other references to past stories.
The last major uprising of the citizens was in the events leading up to The Final Victory, where the people had had enough of Robotnik's reign. This time, the people are fighting to prevent Robotnik returning.
Mekanik, the giant robotic dinosaur from The Rampage of Mekanik returns but is significantly weaker than his debut. This may show that it was because it was of Robotnik's creation this time, rather than Grimer's.
Cedric, the elephant created especially for STC-O by Tom Huxley, makes a cameo appearance as a Badnik (from when he was supposed to be in the Revolution story). If this is to be considered "canon", then it implies that Cedric really does exist.
The comic was largely praised in the Message Zone. Compliments came for its epic nature and nostalgic throwbacks (although many complained there were maybe a few too many). The art was also completely lauded as the best each artist had produced for the comic.
Individual criticisms came from the similarity to Doctor Who finales written by Russell T. Davies (often apocalyptic epics featuring a multitude of characters), despite the story process starting way before the series returned. The story was also expected to bring closure to many stories, such as Robotnik's insanity and Sonic's fugitive status, but seemed to ask more questions than it answered.
The last story to take place before The Battle For Mobius is "Brotherhood", in the 2009 Summer Special. The last stories published before Battle were the Back to School Special's "Road Race" and last part of "Vichama Is Coming Home", due to delays with both strips; both are set earlier.