Spirit Fragments

Soul Fragments are an important plot device in Hyrule Warriors. They are 4 pieces of Spirit of Evil's soul that was separated and placed under seal after the Demon King was defeated by an incarnation of Link, thus ending the cycle of endless conflicts and battles over the Triforce. Three of the Fragments where placed under seal in different eras, while the fourth and final piece was placed under seal by the Master Sword in the Temple of the Sacred Sword.

Story
However part of the Demon King's soul remained free and eventually managed possess and corrupt the Guardian of Time, transforming her into Cia after driving the light from her heart and grants her the Triforce of Power. Cia was then manipulated by the evil spirit into opening the Gate of Souls, summoning monsters from across the ages to serve her, leading to the creation of the Cia's Dark Forces, which brought war to the land of Hyrule. During a battle between her forces and the Hyrulean Forces in the Valley of Seers, Cia manages to steal the Triforce of Wisdom and Triforce of Courage, obtaining the complete Triforce. The spirit then manipulated Cia into using the Triforce to warp time and space creating gateways to the 3 different eras where the 3 fragments where held. Breaking the seals on each of the three fragments, Cia drew them into her body granting her greater dark power.

After the Hyrulean Forces managed to close the gate in each era and Cia's defeated by Midna and Lana in the Palace of Twilight, the fragments left Cia's body and combined together restoring the physical body of none other than the Demon King, Ganondorf. Ganondorf reveals he had manipulated Cia into freeing the 3 fragments of his soul and revealed that he planned free the fourth and final fragment himself once he had taken the Triforce from Cia. However Cia sent the Triforce of Courage and Triforce of Wisdom back to Link and Zelda, catching Ganondorf off guard, allowing her to briefly seal him with a Magic Circle.

The final fragment remained under seal by the Master Sword, until Link removed it from its pedestal at the behest of Princess Zelda in order to defeat Cia and her Dark Forces. However the magic barrier around the Temple of the Sacred Sword kept the Fragment managed to keep it temporarily keep it under seal.

However following Cia's defeat and death, Link did not return the Master Sword to its pedestal and the barrier containing it eventually broke without the power of the Master Sword to keep it contained, allowing Ganondorf to fully restore himself.