The party attacks the Skyhold and kills Janne and Nikolai, both revealed to oppose the Orthodoxy due to its past corruption.

Meanwhile, the Kaiser forces AgnГЁs to dispel the shield around the Water Crystal and overcharge it to summon the Holy Pillar. The group hurries to Florem to intercept the Empire at the Water Crystal, where the man with the purple pen reveals himself to be a Celestial Being named Altair who has possessed Tiz after the Soulstone containing his soul was given to Tiz by the party during his sleep in the vivipod at Eternian Central Command. At the Fire Temple in Eisenberg, following their encounter with the mysterious Kyubi, the group find the Fire Crystal has been overcharged and realize that the Kaiser is summoning the Holy Pillar. The party also learns about the Sword of the Brave, a cursed sword that took Yew's older half-brother Denys' right arm after he tried to claim it he was disinherited and vanished soon after. During their travels, the Kaiser obtains a compass of space and time. With the guidance of both AgnГЁs and a mysterious 'man with a purple pen', the party pursues the Skyhold across the world. The group is unable to prevent the Kaiser from escaping in the Skyhold.

Later guided by AgnГЁs through a crystal shard she dropped when she was kidnapped, Yew assembles three companions: Eternian Ducal Guard captain Edea Lee, the daughter of Braev who aided AgnГЁs in their first adventure, Magnolia Arch, a young Ba'al Buster from the moon who is the sole survivor of an attack on her village and possesses an hourglass capable of localized time manipulation, and Tiz Arrior, a former comrade of AgnГЁs and Edea who has been comatose for the past two and a half years. However, Janne and Nikolai are revealed to be moles for the Empire. Yew Geneolgia, leader of AgnГЁs' Crystalguard protectors, awakens a week after the attack and sets out to rescue her with fellow Crystalguard leaders Janne Engarde and Nikolai Nikolanikov. The ceremony is interrupted by Kaiser Oblivion, leader of the Glanz Empire, and his cryst-fairy companion Anne, who abduct AgnГЁs and imprison her in their floating fortress, the Skyhold. She and Grand Marshal Braev Lee of the Duchy of Eternia seek to end hostilities between their groups with a formal peace treaty in the city of Gathelatio.

Two and a half years after the events of Bravely Default, AgnГЁs Oblige has been elected the Pope of the Crystal Orthodoxy. A similar feature to the first game's reconstruction of Norende also appears, but this time involves rebuilding Magnolia's homeland on the moon. This locks out the other asterisk until much further progress has been made. The asterisk is usually held by another character in game world with that class.Д«ravely Default 's sidequests have been revamped players encounter two Eternian asterisk holders in an argument about an ethical dilemma, and the player must resolve the conflict with the reward being the loser's asterisk. Each character has access to many different Jobs (up to a total of 30) by gaining that Job's asterisk. This also allows the player to level up each character's 'Job Points' (JP).

Players can receive up to three times the amount of experience and money. New to the game is a chain-battle feature where a player who defeats a random encounter may continue to battle enemies in succession for greater risks and rewards. On any turn, characters can 'Default', or guard, and gain an additional Brave Points, or BP, to act multiple times on the same turn. This allows players to build up 'Brave Points' (BP), or the number of user turns per character at any given time. Bravely Second is a traditional role-playing video game with turn-based action, and retains the battle system of its predecessor Bravely Default.

Bravely second code