Botanic Base appears to be a giant greenhouse filled with many plants. The stage includes elevators and doors that lead to rooms containing various power ups. At the end of Level 5, Dr. Robotnik decides to battle the Chaotix face to face.
Dr. Robotnik starts off the battle by shooting the ground causing it to crumble. Robotnik then uses his machine to trap the player's partner at the top of the screen, forcing the player use the elastic force of the ring bond to attack Robotnik in another machine that revolves from one side of the stage to another. To make matter worse, Robotnik shields his machine with electricity, meaning careful timing is needed to strike without dealing damage to yourself. Being attacked by Robotnik's machine will cause your partner to be temporarily released, allowing you attack Robotnik in a more conventional way. The battle ends when the machine is destroyed, releasing the Dark Ring that was powering the machine, causing Robotnik to flee in his machine.