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The third Atomic Destroyer Zone boss is the final boss of Sonic the Hedgehog Triple Trouble. After numerous sub-bosses in the game, the player will have to face the last machine created by Dr. Robotnik in the end of Atomic Destroyer Zone Act 3. During the game, the player has to hit Robotnik eight hits to destroy the chamber completely.
Once destroying all attachments and vehicles created by Robotnik, the doctor himself escapes to the core chamber of Atomic Destroyer Zone, where he has one card up his sleeve to use the chamber to annihilate Sonic/Tails.
During the final battle, Robotnik's pod will constantly shift up and down between the two ends of an electricity chamber. Energy bolts are seen firing from the ceiling of the chamber above the player, which the player should keep avoiding. The player is able to keep hitting Robotnik from the side, when he/she is getting a chance. However if the player tries to attack below or above while the doctor is moving, he/she will get damaged. Eventually the pod's shifting speed decreases slowly and eventually stops to one side of the chamber. If the player starts staying around the center of chamber, the entire room is periodically filled with lightning, that can damage the player. The only way for Sonic or Tails to dodge is to hide inside whichever chute Robotnik isn't occupying at the time.
If the player manages to hit Robotnik eight times, the chamber's activity stops and the doctor himself runs away, with Sonic or Tails on his tail. The player has finally defeated all four bosses at Atomic Destroyer Zone Act 3 and cleared the game.
After the battle, Robotnik then jumps to the closest platform, while player hits him one more time, as the player got the last Chaos Emerald, which Robotnik had obtained earlier in the game. After this, platforms fall along with Robotnik and the player heads to the prison unit to free Knuckles, who has gotten himself captured after the battle against him. Both Sonic/Tails and Knuckles settle their misunderstandings by shaking the hands and then getting out the base.
After this, the game is cleared. Depending if the player has cleared all Special Stages and got Chaos Emeralds, the game progresses to the end credits showing Sonic and Tails flying with the Tornado to the next destination on sunrise. If not, credits screen doesn't appear, but instead showing Fang the Sniper launching and clumsily running away, while dropping five Chaos Emeralds to the ground with words "Try Again" popping up on the screen.