Every Team has 14 missions, plus 2 vs matches, 3 boss battles, and 2 Robot Storms. Most of them are pretty straightforward, but every mission (except for the 7 Bosses) has an extra mission. Usually they allow the level to be more nerve-wrecking, and every team's extra mission is unique to the team. Team Sonic's X-missions have to do with getting to the goal ring within a certain time; Team Dark has to destroy 100 Enemies of any kind; Team Rose has to collect 200 Rings; and Team Chaotix either has to: Collect all items in a level if it's "Collect the Item"; Get to the Goal Ring in a certain time if it's "Get to the Goal ring"; get through undetected in "Find the Special Item"; or finish within the time limit as well as "Finish Undetected."
Stage 00: Sea Gate (Tutorial)===
This in this stage, the player is guided by Omochao through an explanation of how to play Sonic Heroes. Playable only by Team Sonic or Team Rose. (It's a requirement for Team Rose, but it's optional for Team Sonic.)
"Seaside hill" is a seperated,island-like world."According to Tails it's a great vacation spot.
Stage 02: Ocean Palace
- Team Sonic: Get to the Goal Ring / within 5 minutes
- Team Dark: Get to the Goal Ring
- Team Rose: Get to the Goal Ring
- Team Chaotix: Rescue the Chao in the palace / without being detected
Boss: Egg Hawk
A fight against a giant hawk-shaped airship as it flies around a circular highway. Players can damage several sections on the wings, but only need to damage Dr. Eggman directly if they want to win.
Stage 03: Grand Metropolis
- Team Sonic: Get to the Goal Ring / within 5 minutes
- Team Dark: Get to the Goal Ring
- Team Rose: Get to the Goal Ring
- Team Chaotix: Defeat all 85 enemies / within 8 minutes
Stage 04: Power Plant
- Team Sonic: Get to the Goal Ring / within 9 minutes
- Team Dark: Get to the Goal Ring
- Team Rose: Get to the Goal Ring
- Team Chaotix: Defeat 3 Gold Camerons / Defeat the 5 Gold Camerons
Boss: Team Versus
- Team Sonic: versus Team Rose.
- Team Dark: versus Team Chaotix.
- Team Rose: versus Team Sonic.
- Team Chaotix: versus Team Dark.
Stage 05: Casino Park
- Team Sonic: Get to the Goal Ring / within 5 minutes
- Team Dark: Get to the Goal Ring
- Team Rose: Get to the Goal Ring
- Team Chaotix: Collect 200 Rings / Collect 500 Rings
Stage 06: BINGO Highway
- Team Sonic: Get to the Goal Ring / within 6 minutes
- Team Dark: Get to the Goal Ring
- Team Rose: Get to the Goal Ring
- Team Chaotix: Collect 10 casino chips / Collect all 20 casino chips
Boss: Robot Carnival
- Team Sonic: Defeat 12 waves of enemies.
- Team Dark: Defeat 12 waves of enemies.
- Team Rose: Defeat 8 waves of enemies.
- Team Chaotix: Defeat 12 waves of enemies.
Stage 07: Rail Canyon
- Team Sonic: Get to the Goal Ring / within 5 minutes
- Team Dark: Get to the Goal Ring
- Team Rose: Get to the Goal Ring
- Team Chaotix: Get to the Goal Ring / within 6 minutes
Stage 08: Bullet Station
- Team Sonic: Get to the Goal Ring / within 6 minutes
- Team Dark: Get to the Goal Ring
- Team Rose: Get to the Goal Ring
- Team Chaotix: Destroy 30 capsules / Destroy all 50 capsules
Boss: Egg Albatross
A fight against a giant hawk-shaped airship as it flies around a circular highway. Players can damage several sections on the wings, but only need to damage Dr. Eggman directly if they want to win.
Stage 09: Frog Forest
- Team Sonic: Get to the Goal Ring / Get to the Goal Ring within 5 minutes
- Team Dark: Get to the Goal Ring / Defeat 100 enemies
- Team Rose: Get to the Goal Ring / Collect 200 Rings
- Team Chaotix: Get to the Goal Ring without alerting frogs / Get to the Goal Ring within 4 minutes without alerting frogs
Stage 10: Lost Jungle
- Team Sonic: Get to the Goal Ring / within 6 minutes
- Team Dark: Get to the Goal Ring
- Team Rose: Get to the Goal Ring
- Team Chaotix: Find 10 Chao / Find all 20 Chao
Boss: Team Versus
- Team Sonic: versus Team Dark.
- Team Dark: versus Team Sonic.
- Team Rose: versus Team Chaotix.
- Team Chaotix: versus Team Rose.
Stage 11: Hang Castle
- Team Sonic: Get to the Goal Ring / within 6 minutes
- Team Dark: Get to the Goal Ring
- Team Rose: Get to the Goal Ring
- Team Chaotix: Find 10 keys / without being detected
Stage 12: Mystic Mansion
- Team Sonic: Get to the Goal Ring / within 7 minutes
- Team Dark: Get to the Goal Ring
- Team Rose: Get to the Goal Ring
- Team Chaotix: Blow out all 60 red torches / Blow out all 46 blue torches
Boss: Robot Storm
- Team Sonic: Defeat 13 waves of enemies.
- Team Dark: Defeat 14 waves of enemies.
- Team Rose: Defeat 6 waves of enemies.
- Team Chaotix: Defeat 14 waves of enemies.
Stage 13: Egg Fleet
- Team Sonic: Get to the Goal Ring / within 9 minutes
- Team Dark: Get to the Goal Ring
- Team Rose: Get to the Goal Ring
- Team Chaotix: Get to the Goal Ring without being detected / within 6 minutes
Stage 14: Final Fortress
- Team Sonic: Get to the Goal Ring / within 9 minutes
- Team Dark: Get to the Goal Ring
- Team Rose: Get to the Goal Ring
- Team Chaotix: Find the 5 keys / Find the 10 keys
Boss: Egg Emperor
A fight against Eggman in a giant armored Eggpawn Mech. Players must strike the multi-colored Eggman orb in the center of the Egg Emperor's armor to win.
Last Boss Ver. 1: Metal Madness
Team Rose,Team Chaotix and Team Dark fights against Metal Sonic, who has transformed himself into a hideous beast, using the power of Perfect Chaos.
Last Boss Ver. 2: Metal Overlord
Team Super Sonic fights against a further mutated Metal Sonic, who has now gained the ability to fly.