The Crystal Chalice is used to carry drops of Myrrh. Large Crystals protect the people in the world from the Miasma that plagues it, but this protection wears off over time. Drops of Myrrh are needed each year from Myrrh Trees to renew the Crystals. Caravans from each village and city must collect these drops with the Crystal Chalice.
The Chalice also contains a shard of a crystal to protect the members of the Caravan when traveling through the Miasma. In Multi-player Mode, one player must carry the Chalice around when in a dungeon, and in Single Mode, a moogle named Mog carries it around. Each Miasma Stream has an element which changes each year and can only be passed if the Chalice contains the same element.
The Element of the Chalice can be changed from Fire, Water, Wind, and Earth. The player can change the element of the chalice by using different Hot Spots. These Hot Spots are located throughout the dungeon and can either be used to change the element or teleport the party out of the dungeon.
There is a special Mystery Element that the player can obtain by completing various tasks in the Lynari Desert. This element will allow the player to pass through any Miasma stream without having to change the chalice to the element of the steam's.
The Crystal Chalice's element will not only allow the Caravan to pass through Miasma streams, but it will also protect the party from various status ailments:
- Earth: When the element is changed to Earth, the Caravan is protected from the Poison and Petrification status effects.
- Wind: If the element is changed to Wind, the party will receive protection from the paralysis that the Thunder spell causes.
- Fire: The Fire element guards against the burn that is caused from a Fire spell.
- Water: When the element of the chalice is Water, then the party will not be frozen when an enemy casts a Ice-based spell.
- ???: If the element of the Chalice is the Lynari Deserts white Mystery Element, it will allow the Caravan to pass through any Miasma stream but it provides no protection.
- Note: The Fire, Wind, and Water elements will only protects the player from the basic spells. For protection for -"ra" and -"ga" spells, one will need armor and accessories that guard against that element.
A Crystal Cycle is completed when the Caravan collects one drop of Myrrh from the Myrrh Tree after defeating the boss of that tree's dungeon. The Caravan cannot receive another drop of Myrrh until the Myrrh Tree replenishes itself after two years have passed. The level and its monsters become increasingly difficult with each passing Crystal Cycle.
Certain dungeons of rooms filled with a poisonous gas, much like the Miasma from the original game. The Lilties' urn can be set on certain tiles that create a sphere around it to protect all party members inside the sphere from the gas, much like the Crystal Chalice from the original game. Failure to protect oneself will result in a quick death for the player.
There is a sculpture of a Crystal Chalice in the Alfitaria Royal Library.