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- The party are referred to as Warriors of Light, a recurring motif in the series, near the end of the game storyline.
- In order to awaken the Earth Crystal the undead monster Gigas Lich must be defeated. It correlates with the events of the original Final Fantasy where the Warriors of Light must defeat Lich, an undead monster, to return light to the Crystal.
- Similarly to Final Fantasy III, the first elemental crystal to be encountered is the Crystal of Wind.
- Tiz's Onion Shirt costume is modeled after the Onion Knight's 3D remake design.
- Olivia Oblige takes a fatal blow for Agnès and the party prior to their awakening the Water Crystal, alluding to Aria Benett doing the same for the Warriors of Light. Olivia and Aria are both guardians for the Water Crystal.
- The Summoner and Conjurer asterisks reference the Evoker and Summoner jobs from Final Fantasy III. The Summoner focuses on the use of summons with their default functions, similar to the Evoker. The Conjurer allows for the use of summons with a more powerful effect, similar to the Summoner. In addition, both the Summoner of Final Fantasy III and Conjurer of Bravely Default share the same Japanese name: "Demon World Illusionist" (魔界幻士, Makai Genshi?).
- The Drunken Pig pub aboard Grandship could be an allusion to the ones in Final Fantasy V. It has a stage with a performing girl similar to the dancing girls and there is a piano on the side of it.
- The depiction of Norende Village's destruction in the opening FMV seems to reference the Light of Judgment sent from Kefka to smite entire towns.
- Ciggma Khint's role as a mercenary resembles that of Shadow. Both charge expensive fees for their services, will depart from battle of their own will, and are revealed to be estranged from their daughters.
- Just like in Final Fantasy VI, there is a portion of the game where the player needs to defeat one dragon of each element to unlock a hidden power.
- Qada releasing a poison mist to wipe out enemy forces may allude to Kefka poisoning the water supply of Doma; both acted against the orders of their honor-bound commanding officers and expressed no concern for their own allies getting poisoned in the process.
- There is an officer in the Shieldbearer army named Steiner, and he has a rivalry with a female officer (there is no romantic subplot, however).
- The Adventurer reprises their role as the Save point. The fox companion is also present, but as a shop trader. Both reprise their roles as optional bosses at the end of a bonus dungeon.
- Several bosses who were servants of Chaos appear as Nemeses.
- The boss theme against Nemeses is a rearrangement of "Battle with Monsters" (魔物との戦い, Mamono to no Tatakai?) and "Strong Enemy" (強敵, Kyouteki?), the respective battle and boss themes from The 4 Heroes of Light.
- Normally the Bravely Second: End Layer trailer can be unlocked by completing the game but the player can also unlock it by using the Konami Code ( ) on the title screen.
- The Party Chat feature is an allusion to the skits of the Tales series.
- Victoria F. Stein is likely an allusion to Victorique de Blois of the light novel and anime Gosick. Both characters are young girls of extraordinary intelligence who speak like old women. Alternatively, she and Victor could both be references to Victor Frankenstein, the protagonist of Mary's Shelly's novel Frankenstein.
- Ominas Crowe's obsession with fire, his massacre of his own troops in the Centro Keep with a mass of Fire spells, and the cutscene of him saying Fire, Fire, Fire!!, is very similar to the once controversial pyromanical tendencies and behavior of the character Beavis of the titular duo of Mike Judge's Beavis and Butthead.
- It is strongly suggested that the Celestial Realm Ouroboros sought to infiltrate is the real world. The summoning animations depict modern-day machinery, the Dark Aurora contains floating rubble that resembles street lamps and railroad tracks, and the intervention of various parallel worlds is customized to feature Nintendo 3DS friends the player has registered who are also playing Bravely Default. The player's face may also appear in the battle background when Ouroboros claims to see the Celestial Realm, as the 3DS internal camera is briefly switched on. As Tiz is revealed to house a celestial which he releases at the end, it can be inferred that the celestial is the player, who was able to play the game and aid the party through Tiz. The fairy who appears at the beginning and ending of the game also addresses the player directly, suggesting that she had a role in bringing the celestial to Luxendarc.
- The in game referred long lost nation of Wa is implied to be the real life nation of Japan.
Spoilers end here.