The Labyrinth consists of 2 separate sections. The main dungeon of the game is the Yggdrasil Labyrinth, which encompasses the Yggdrasil Tree that sprouts from High Lagaard, eventually reaching the Heavenly Throne and the floating islands above.
Separate from it is the ruins of Ginnungagap, south of High Lagaard. During Story Mode, the party's main objective is to escort Arianna into the depths of Ginnungagap to conduct the ritual that is to be performed every century, but circumstances of the plot demand the party take some time to advance through the Yggdrasil Labyrinth in order to progress deeper into Ginnungagap.
- See also: Yggdrasil Labyrinth (Etrian Odyssey II)
With the Duke of High Lagaard having fallen ill with a disease, High Lagaard has called for adventuring parties to head into the labyrinth and ascend the tree in hopes of reaching the floating castle above and attaining the Holy Grail, which is said to be able to cure the disease. Exploration of the Labyrinth is secondary to the Story Mode's objectives, but ends up tying in to the plot from time to time.
- 1st Stratum: Ancient Forest (EO2U)
- 2nd Stratum: Auburn Thicket (EO2U)
- 3rd Stratum: Frozen Grounds (EO2U)
- 4th Stratum: Petal Bridge (EO2U)
- 5th Stratum: Heavenly Keep (EO2U)
- 6th Stratum: Forbidden Wood (EO2U)
- 7th Stratum: Dark Paradise (DLC only)
The ruins of an ancient temple, located near High Lagaard. In Story Mode, it is crucial to the plot that the party delves into the ruins to complete the centennial ritual and investigate the anomaly that had happened one century ago. Progress in the Yggdrasil Labyrinth may even be halted until the party has made significant progress investigating the ruins.
In Classic Mode, the ruins are still available to the player, but are only unveiled floor by floor in the form of quests that become available as the player conquers more strata of the Yggdrasil Labyrinth.