03 undoubtedly had the power to destroy all Aragami on the spot. However, she could not stop the Aragami from getting onto her body. If 03 would really want to annihilate the Aragami that managed to get onto her body, her attacks would definitely do some damage to her own base.
The battles over a thousand years had turned the metallic base of the pyramid into ruins. If she could, she would not want to harm her own body as well. Therefore, even when 03 could annihilate the Aragami all by herself, she chose to request aid from Joshua and his friends.
Meanwhile, Joshua had upheld his side of the bargain. He kept his word.
