After Team Dark and Team Chaotix had made their way to the roof of the Power Plant, Rouge notices the Chaotix nearby and suspects that they are out to steal "her" treasure. Espio senses Team Dark nearby and he, Vector and Charmy find themselves faced by said team. While Rouge makes accusations at them, Espio suspects Team Dark are their client's adversary. With both teams thinking of the other as an enemy, a fight quickly ensues.
Watching from above, Team Dark spots Team Sonic passing through the jungle. There, Shadow's curiosity is piqued by the hedgehog that looks like him. Team Sonic quickly notices them and all of the members are both surprised and shocked to see Shadow alive after his supposed death. Not wanting them to get in her way, Rouge tells Team Sonic that their efforts are wasted and that she and her team will take care of Dr. Eggman. However, Sonic does not back down despite a death threat from Omega, and after Sonic and Shadow exchange mocking words, the two teams battle.
The object of these battles is to knock Team Dark off the edges of the battle platforms into the bottomless pits surrounding them. There is no damage system in this boss, meaning Team Dark cannot be defeated by simply damaging them. Grabbing the Power Cores and Rings before the opponents do is crucial. Without Rings, Team Dark will fly back farther, making them easier to be knocked off. Some characters are more suited to battle against specific Team Dark members due to having moves that are most effective against their particular formations:
If the player loses any team members, they can be brought back to the field by performing the Team Blast.
In this arena, there are a total of nine Power Cores; three blue, three yellow, and three red. The player should start by grabbing the Blue Power Core in the center (so Shadow cannot use it). When the other team is near, have Espio use Leaf Swirl to fling them into the air. While they are grounded, they can collect more Power Cores or steal their Rings. Staying aware of the other team's location is key to winning.
If Leaf Swirl does not work, switching to Charmy and shooting them off the edge is an alternative strategy.
— Shadow, before Team Sonic battles him and Team Dark.
In this area, there are only three available Power Cores and they sit outside the arena in balloons. There is also a Shield hidden in a Wooden Container on the stage. For this battle, Team Dark will be much more difficult to defeat as they will always switch to the formation that is dominant over that of the player.
The player should start the battle by having Sonic use Blue Tornado on Team Dark. This will knock them down temporarily. The player should then switch to Tails and use Thunder Shoot to collect the Power Cores in the balloons on the side of the arena, then use Thunder Shoot to keep the Team Dark members down. When a member of Team Dark is downed, the player should switch to Knuckles and use Fire Dunk to knock them off of the edge. Once all three members of the other team are knocked over the edge, the battle is over.
"Step back! Let us get the doctor first." - Shadow before fighting Team Chaotix.
"I'll find Eggman's treasure first!" - Rouge before fighting Team Chaotix.
"Eggman is mine. Get outta our way!" - Omega before fighting Team Chaotix.
"What was with that hedgehog that looked like my twin?" - Shadow before fighting Team Sonic.
"Shadow, Omega, let's go!" - An unused line Rouge would have said before fighting Team Sonic.
"Battle preparation complete. Initiating attack." - An unused line Omega would have said before fighting Team Sonic.
↑This line can be brought back in the PC version with the help of the Sonic Heroes Memory Editor by swapping the position of the Speed character with the position of the Fly character before loading the fight against Team Sonic.
↑This line can be brought back in the PC version with the help of the Sonic Heroes Memory Editor by swapping the position of the Speed character with the position of the Power character before loading the fight against Team Sonic.