Sonic's story sees the blue blur battling to gather the Chaos Emeralds, with Tails by his side for the most part, to prevent Robotnik destroying Station Square and building a new city, Robotnikland on its ruins, with help from Chaos, an ancient monster made of water capable of absorbing the Chaos Emeralds to strengthen itself, and his new flying fortress, the Egg Carrier.
Tails' story is much like Sonic's, albeit shorter, and there are chunks of the story where Tails undergoes solo missions, having been separated from Sonic.
Knuckles' story sees him hunting down the missing shards of the Master Emerald, which was destroyed when Chaos was released, to return the Floating Island (which was now known as Angel Island) to the skies. It also sees him gaining several insights into the ancient past, when there were more of his people alive, through a sentient ball of light released with Chaos.
Amy's story sees her being hunted down by a malevolent robot named Zero, intent on capturing a Flicky whom she decides to protect, and whose family she later tries to find.
Big the Cat is a new addition to the character roster, and his story, which is more or less separate to the other heroes' struggles sees him chasing down his friend Froggy, whose behaviour has become extremely erratic after growing a strange tail and swallowing a Chaos Emerald.
The robot, E-102 Gamma, is another new character, who only really appeared in this game. His tragic story sees him performing several tasks for Robotnik, before Amy helps him break free from his programming and setting off on a doomed mission to save his organic battery 'friends' by wiping out all E-100 series robots.
Only when all the above characters' stories are complete can the Last story be unlocked, which sees Chaos letting his pent-up rage get the better of him. He breaks away from Robotnik, absorbs all the Chaos Emeralds, ascends to his monstrous Perfect form and floods Station Square. With the help of his friends and Tikal, who explains what happened to enrage Chaos so much, Sonic absorbs the positive power of the Emeralds (while Chaos only absorbs the negative) and duels the monster in a epic battle as Super Sonic.
Sonic Adventure was adapted very loosely in Sonic the Comic in a ten-part story arc which began in Issue 175. As with previous adaptations, the story borrowed from the game while adding numerous elements from the comic's continuity. The Sonic Adventure arc is known for being arguably the darkest story to appear within the pages of the original comic, featuring major character development for Sonic, Knuckles and Robotnik, and the untimely death of Johnny Lightfoot.
The story differs from the game in that Grimer releases Chaos, not Robotnik, Chaos itself is not a once benevolent God turned violent, but a heavily mutated Drakon Prosecutor, the Floating Island falls due to Knuckles ejecting the Emeralds from the island rather than the Master Emerald being destroyed, Big only has a passing appearance and is lacking Froggy, Gamma is not present at all, and when Super Sonic makes an appearance, he is still a pacifist, but it doesn't last long.
Elements from Sonic Adventure were also used in Sonic the Comic Online.
In Sonic the Comic, only two locations from the game were used: The Floating Island, which continues to use the Emerald Chamber to house the Master Emerald, as opposed to an altar, and the Echidnas' main city, which is shown as Megopolis City in its glory days.
In Sonic the Comic Online, the Egg Carrier makes an appearance as the mobile headquarters of the Syndicate, albeit with the ship's name changed to the more imposing Death Carrier. Emerald Coast, the first level players visit, is revealed to be the resting place of the Death Egg in Return to the Death Egg.
In keeping with Sega's redesigns of the characters, Sonic and the Freedom Fighters are given new looks, in the form of coloured irises. Their general proportions remain the same though, as opposed to the game's lanky, differently proportioned renditions of the characters. Sonic's appearance is the first to change, and the others gain coloured irises two issues later, though it is not explained why. Robotnik changes too, swapping out his Adventures of Sonic the Hedgehog outfit for a jacket and trousers resembling his new in-game counterpart. The characters' appearances have remained this way since. In Sonic the Comic Online, Big the Cat has come into prominence too, having shifted from a mere cameo role to having his own roles to play in several stories, and even having a story centred around him.