When the universe was created, it was divided into darkness and light. As the light waves consumed the world, the darkness filled the universe and eliminated the chaotic light, allowing life to flourish. However, the Light of Destruction threatened to invade the Gentle Darkness and destroy all life. The one who had power strong enough to defeat the Light and protect the Darkness was the Supreme King.
The King informed Yubel that a certain individual held the power of the Gentle Darkness, and that he needed a guardian to watch over him until he grew to adulthood and could control his power. Yubel volunteered to be that guardian, and was transformed from a human into a Duel Monster Spirit. The purpose of the Gentle Darkness inside the Supreme King is to combat the malignant Light of Destruction.
Although it wasn't referred by its actual name, this power was mentioned in season 1. Amnael knew that Jaden had dormant powers which even Jaden himself was unaware of and which had yet to be awakened. He believed it could stop the Sacred Beasts. Kagemaru claimed that it was "the mightiest power to control the spirits". That is the reason why he chose Jaden to be his opponent.