The objective of the tower is to defeat a substantial number of boss enemies. Each is sorted into its own dungeon, with Stamina only being consumed upon victory. Roaming Warriors are forbidden, but the player can call on Dr. Mog for aid in place of a Roaming Warrior.
The unique gimmick of the Crystal Tower is that when a player defeats a boss, the party members they used are forbidden from being used against the other bosses. This means the player must have a number of high-powered characters in order to complete the tower. The player may refight a boss to change the forbidden party members to those in the new party used, freeing up the old ones. Upon defeating all the present bosses the player is given a victory screen showing the party they used in each fight.
While there is no penalty for aborting attempts or fleeing from a boss, Cid's Missions rewards are given out to players who can beat Crystal Tower bosses without aborting the attempt, with more rewards given out the more bosses the player defeats. Additionally, each dungeon has its own Mastery and First Time rewards, that the player can earn the same as any other dungeon; Mastering a dungeon is not necessary to complete the Crystal Tower, and as the player can attempt the Crystal Tower as much as they want, they can retry the boss for Mastery completion at a later time.
This first-time run of the Crystal Tower differed slightly from later runs; there were five bosses, not four, and completing all of them allowed the player to fight a final boss using any combination of the characters used to defeat the first five bosses. It also featured Normal and Hard versions of the bosses, and Bravery Synergy was rewarded based on combat roles, not the boss' home realm.
While not classified as a Crystal Tower-type dungeon, the special "Protect the Espers" event utilized identical mechanics. All Warriors from all realms gained Realm Synergy in this event. The event later gained a Hard version, but this version featured a different set of enemies.