Sonic Heroes' story is split into five segments, each intertwining in some way.
Team Sonic's story focuses on Sonic, Tails and Knuckles chasing Dr Robotnik around the world, having undertaken his personal challenge of trying to stop him before he conquers the world in three days.
Team Dark's story focuses on the anti-heroes of Sonic's world, seeking answers. In search of Robotnik's secret treasure, Rouge the Bat stumbles upon a still-alive, albeit amnesiac Shadow the Hedgehog, and a vengeful robot named E-123 Omega, and the three team up to track Robotnik down.
Team Rose's story follows Amy Rose, Cream the Rabbit and Big the Cat in their quest to find those important to them. Cream seeks Cheese's brother, Chocola, Big has lost Froggy again, and Amy is only after Sonic, who, according to a newspaper article, was last seen with Froggy and Chocola.
Team Chaotix's story sees the dysfunctional detectives performing a number of missions for their newest client, who is only communicating with them through a radio.
The final story, taking a leaf from Sonic Adventure and Sonic Adventure 2, sees all four teams coming together to take on a heavily upgraded Metal Sonic. It can only be unlocked when all four previous stories have been completed, and the Chaos Emeralds have been collected.
In a series first, Sonic Heroes gives the player control of three characters at once, with one at a time leading formation. Each character conforms to a set type, said types being Speed, Power and Fly. Speed characters can create tornados which can remove armour and stun enemies, as well as jump between walls in narrow spaces. Power characters can break through barricades and link up with allies in a gliding manouevre, and Fly characters can reach new heights and hit targets their teammates can't reach. The heroes can also increase the strength of their attacks through levelling up. Heroes also marks the return of the Special Zone to the series.
Sonic Heroes has had a very loose adaptation in Sonic the Comic Online, in the form of Sonic the Hedgehog's fall from grace. Sonic's reputation rapidly goes downhill after a slanderous documentary appears, courtesy of the Kane Broadcasting Company. In the following weeks, Sonic finds himself repeatedly framed, and the people of Mobius are quick to turn against the hero. Eventually, Sonic is imprisoned, and swiftly replaced by a sadistic shapeshifting doppelganger, later revealed to be a Neo Metallix, who Sonic battles in the caves beneath the Hill Top Zone. Fans were unaware that the story arc was an adaptation of the game until the appearance of Metallix. Sonic Heroes was reviewed in Issue 229, where it recieved an overall score of 93, the review calling it 'fast, thrilling and immensely fun' but criticising the repetitive level designs. Much of the fanbase were less kind however.
After the release of Sonic Heroes, two prominent spin-off message boards were created from STC Online to work off the tensions between the in-game teams. Team Sonic and Team Dark were the prominent communities, with the latter still containing posting members as of 2011.