Two and a half years after the events of Bravely Default, Agnès Oblige has been elected the Pope of the Crystal Orthodoxy. She and Grand Marshal Braev Lee of the Duchy of Eternia seek to end hostilities between their groups with a formal peace treaty. But the ceremony is interrupted by Kaiser Oblivion, leader of the Glanz Empire, who abduct Agnès while defeating those present. Yew Geneolgia, leader of Agnès' bodyguard unit, the Crystalguard, awakens a week after the attack. He sets out with fellow Crystalguard leaders Janne Engarde and Nikolai Nikolanikov to rescue Agnès. When they regroup with their comrades, Nikolai returns home to heal wounded soldiers. That night, Janne murders the remaining Crystalguard survivors and reveals he has been with the empire from the start. Yew escapes and returns home only to discover that Nikolai has apparently been killed in a follow-up attack by imperial forces. Afterwards, guided by Agnès through a crystal shard she dropped when she was kidnapped, Yew gains a companion in the Eternian Ducal Guard captain Edea Lee, the daughter of Braev who aided Agnès in their first adventure. On the way to Eternian Central Command to revive Tiz Arrior, a former comrade of Agnès and Edea who entered a deep coma for the past two and a half years, Yew is joined by 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. Though group manage to revive Tiz, they are too late to stop the Kaiser from escaping in his Skyhold air fortress while learning that Nikolai faked his death and also serves the empire.
With Agnès' aid, the party pursues the Skyhold to the Harena region, making a stop at Yew's school day home of Al-Khampis. There, the party learns of a giant creature called a Ba'al who fell from the sky some time ago and currently lies dormant in what remained of the Kustra Archipelgo. After arriving there and seeing the Ba'al is missing, Magnolia reveals it to be her quarry after it ravaged her home and that she sensed it on the Skyhold with the Kaiser. Upon returning to Al-Khampis, the party meets the highly regarded scholar Professor Norzen, revealed to be the one who gave Edea the means to revive Tiz. After losing to the group when he attempted to destroy the Skyhold at the cost of Anchiem, Norzen explains that the Kaizer is searching for a "compass of space and time" and implores the group with his dying breath when assassinated by Minette Napkatti. The group locates the compass, but Minette steals it and dies handing it to Janne. The group encounters Janne again, who reveals himself to be the last survivor of House Balestra, a family that served in the Crystalguard 16 years ago until their opposition to the Orthodoxy surrendering to the nascent Duchy. Janne reveals he intends to avenge his father's death at the hand of Yew's father before taking his leave on the Skyhold as it travels to Eisenberg.
In Eisenberg, the party runs into a princess named Yoko as they help her find her brother Danzaburo. The party attends a festival in the city of Hartschild held by a baker named Angelo, where Magnolia and Yew bond. The next day, finding Hartschild empty, the group attempt to reach Yunohana before Yoko is wounded by the Glanz Empire's sniper Aimee Matchlock. While recovering in Yunohana, Yoko reveals Danzaburo is searching for the Sword of the Brave to legitimize his inheritance. Yew reluctantly reveals the sword's location and the group arrive too late to stop her as she claims the sword with the weapon taking Danzaburo's sword arm as payment. This horrifies Yew, who reveals that he caused a similar tragedy with his older half-brother Denys Genelogia who left soon after. But Yoko reveals Danazburo is an illusion while assuming her true form as a yokai, proceeding to torment the group before Alternis appears to drive her off. But Yoko leaves out of whim while telling the group to go to the Fire Crystal temple to discover the Kaiser's true goal. At the Fire temple, Tiz and Edea discover that the Fire Crystal has been overcharged as the group realize his goal to summon the Holy Pillar. After defeating Janne, restoring Hartshield's people after learning Angelo is a member of the empire, the group hurries to Florem to intercept their enemy at the Water Crystal, only to see the Skyhold shot down by a massive energy blast.
The group consults the matriarch of Florem and has the Vestling of Water, Sylvie, place a shield around the Water Crystal. The group then repels an attack by the Glanz Empire's Geist Grace while attracting the attention of Lotus, an engineer from the hidden Sagitta Village. He takes the party to Sagitta and reveals their Ba'al destroying SP cannon, revealed to be the weapon that grounded the Skyhold after they detected a Ba'al within it. The party also learn the identity of their mysterious benefactor to be Altair, a Celestial Being who possessed Tiz since the Great Chasm and remained quiet until ending up in the youth's body a second time to guide the group. He reveals that the Ba'als are being created from his memories. Meanwhile, revealed to have manipulated her through Geist's son Revenant Grace, the Kaiser has Agnès dispel the shield around the Water Crystal and overcharge it to summon the Holy Pillar. After defeating Geist and Nikolai, both following the Kaiser out of their respective guilt, the group decide to mount an assault on the Skyhold. But with Revenant and Janne sacrificing themselves to slow the group down, the Kaiser takes Agnès with him as he travels back in time. No sooner did the Kaiser leave then his cryst-fairy aide Anne uses the Holy Pillar's power to remove the Moon. The party defeats Anne in battle, but the destruction of the Moon ceases the flow of time and places the world in a state that would eventually end in inevitable destruction.
The party uses Magnolia's hourglass to go back in time to the peace ceremony and stop the Kaiser from abducting Agnès, only to learn the man is Yew's estranged older brother Denys Geneolgia. As Denys is later freed by Janne and Nikolai, everyone finds they have some memory of the previous timeline so Yew's group secures the compass and orchestrate a plan to damage the Skyhold. Yew's group also confront all of Denys' lieutenants, sparing their lives while convincing them to turn over a new leaf, only to find Denys escaped to the Genelogia crypt. Yew eventually corners Denys, learning his brother's intent to use the compass to travel back in time to kill their family's founder Fondar Genelogia to negate the corrupt misdeeds caused by his bloodline. But Yew defeats Denys while convincing him that his way would not solve anything. Though Denys accepts any punishment upon his lost, Agnès and Braev convince him to own up to his mistakes and create a world of peace in the present. But the celebration is short-lived when the party learn that Anne used Sylvie to manifest the Holy Pillar to once more remove the moon. Though Denys destroys Anne's brooch, the fairy having revealed to have intended to betray him, she awakens the Ba'al that ravaged Magnolia's home from within the Skyhold to destroy the group. When Diamante proves too much for Yew's group to defeat, Denys sacrifices himself by using the compass to send himself and the Ba'al to the end of time itself.
The party awakens in Caldisla, which was revealed to have been removed from everyone's memory by Yoko until that moment. After a Ba'al attack, the group find Anne at the Great Chasm of Norende where she began to summon peak condition Ba'als through. Prior to her defeat, Anne is revealed to be the older sister of Airy and that she helped Tiz and the others eliminate her and Ouroboros since their intrusion on the Celestial Realm posed a threat to her master Providence. Called a god of the Celestial Realm, Anne explains that the Ba'al were created by Providence using the memories of Altair's lover Vega. After Anne is killed, the group enters the Celestial Realm while Altair recounts his time with Vega before finding her and freeing her from Providence's control. But after Altair and Vega depart in peace, the group are attacked by Providence, who reveals that they are controlled by another being (The Player) while nearly manipulating that being into destroying itself (delete the save file). But Yew stops the being as he and the others who got given second chances convince that figure to not give up before the group destroy Providence.
When the group return to Luxendarc, Tiz is revealed to be dying again now that Altair's soul has left him. But the mysterious Adventurer, who has provided aid to the party, appears and takes Magnolia's hourglass back in time to give to Tiz at the start of his original adventure. The Adventurer, revealing herself to be a colleague of Altair's named Deneb, returns and informs the group that the hourglass, now with two and a half years' worth of hopes and dreams, will be able to renew his life. Agnès, possessing the hourglass, delivers it to the party and revives Tiz. Some time after fulfilling her goals, Agnès retires from her duties as the pope and settles down in Norende with Tiz while Edea sets out as the new Grand Marshall to secure the peace between Eternia and the Orthodoxy. At that time, Magnolia decides to remain on Luxendarc with Yew finally working up the courage to confess his love for her and returns the expression by telling him him her true name. In a post-credits scene, having posed as Alternis Dim to aid his friends from behind the scenes, Ringabel is revealed to have become an agent of an interdimensional police force called the Planeswalkers and confirms to them that the Sword of the Brave exists.
