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The key beating the Ancient Dragon is simply to ensure that you have sturdy defenses protecting your crystals during the final boss wave. These defenses must require little to no repair maintenance as most of your attention must be directed towards the boss (this strategy applies to Nightmare as well). This way while you are running to the harpoon torpedoes you, you don't have to worry about your crystals. Usually the dragon will do the same pattern over again. Just learn his pattern and beat him to the torpedoes. For more information see Ancient Dragon