According to Grune, the Cradle of Time is the place where time begins and ends, and as such, the area exists in in a different space-time continuum from Shining Blue. The Cradle of Time can only be entered through the Altar of the Sea after the group receives "Super Sacred Eres" from Nerifes. From the altar, the area appears a swirling pattern in the sky. The entrance is a dirty trail full of rocks, a few trees, and a teleportation pad at the end that leads to the next area. The following area is a series of repeating islands with distorted buildings molded together that hold some of the previous bosses from the both the Main Quest and Character Quests. After defeating all thirteen bosses within, the group is allowed to return to the entrance and heal. The final area, where Schwartz waits for the group, is a small island on the very distance of the cradle.
Senel Coolidge and his companions travel to the Cradle of Time in order to stop Schwartz. During this time, Schwartz waits within the Cradle of Time and rests in preparation to play the "Melody of the End" that will guide humankind to nothingness. When the group arrives, Grune asks the others if they would like to go back, but they tell her they going to finish what they came there to do. At the first teleportation pad, the black mist appears then vanishes, and Grune explains that numerous monsters will be waiting on each level to fight them. When the group arrives in the next area, they are attacked by previous bosses they defeated before. The first six levels include the "Citadel Turtle" from the Waterways; "Zephyr Lucifer" from Mirage Palace; "Chariot Gaet", "Silver Galf", and "Gold Galf" from the Hidden Fortress; "Diva" from the Man Eating Ruins; and "Dinowyrm" from the Secret Passage.
When the group arrives at the next level, Grune holds them back because she feels a strong concentration of grief and sadness. After "Dark Senel" and "Dark Shirley" appear before the group, Shirley Fennes sees this image as her old self that fell into her weakness. After defeating their shadows, Senel and Shirley manage to use their Sacred Eres to put a rest to their past selves and move forward to the next levels of battles. The next six levels include "Fenrir" from The Crags; "Beezlebub" from Secret Passage; "Grand Gaet" from the Great Hollow; "Dragon" from the Front Line base; "Crystarantula" from the Crystal Forest; and "Royal Automaton" from the Wings of Light. After this, the group is able to challenge Schwartz for the final battle.
When the group arrives to the area where Schwartz is, she asks them why they are trying to save their world. However, their explanations only anger her, and she attacks them. After a long battle with Schwartz, she suddenly stops and the exhausted group begins to believe that their attacks are doing nothing. Schwartz tells them that she shall be the planet's savior, but Grune tells her she is wrong. Schwartz, believing that humans have rotted Grune's thoughts, finds her now worthless. Schwartz then unleashes the black mist across the Legacy and sends replicas of herself to attack its civilians.
With another attack intended to kill the group, Grune jumps in front of the blow and attempts to subdue its power. The group begins using their powers to assist Grune and manage to prevent the attack, but after such exertion, their power weakens as Schwartz seemingly grows stronger. She attempts to attack the group again, but Grune blocks the blow once more, which inspires the group to keep fighting. Their courage convinces Nerfies to grant the people of the Legacy Sacred Eres of their own to defeat the Schwartz clones. Unrelenting, Schwartz promises to return the world to void and faces the group a final time before being defeated. After her defeat, Schwartz's mask is severed in half, revealing that she is merely an incarnation of Grune. As she begins to disappear, she warns the group that she is born from the deeds of humans and will return. The group then returns to the Altar of the Sea, unaware of the outcome of their recent battle.
- The Cradle of Time is one of three dungeons in the game not accessible from the World Map. Both Mirage Palace and the Wings of Light are connected by the surviving remnants of the ancient tram system. The Cradle of Time can only be reached through a portal at the Altar of the Sea.