Phantom Brave: We Meet Again plays a lot like other isometric, conditional turn-based strategy RPGs (Final Fantasy Tactics, Disgaea, etc.), but with noticeable changes. For example, the game is not 100% isometric, as the camera can be rotated eight-ways and features three levels of camera zoom (although the player can only attack from the closest two). Also, movement and attacks are not limited to a grid system; attacks can be performed over a certain range (and, depending on the attack, encompass multiple enemies), and movement is relative to where the character is standing. Each character is given a set number of movement points which define how far they can go in one move; however, with clever use of the physics engine, it is entirely possible to move much further than you potentially could in one move.
At the beginning of each battle, Marona must confine a set number of characters to nearby objects. This number changes depending on whether or not the confined character is carrying an item, since the item must be summoned, too. Characters then fight for a certain number of turns before exiting the board, unable to be confined again for the remainder of the battle. Dead characters are paused on the number of turns they had left when they died, but their dead bodies can continue to be attacked until they are destroyed, which has the same affect as if that character ran out of turns. They can be revived after battle, but require an item to do so, as do items that are destroyed under the same circumstances.
In addition to killing enemies traditionally, characters can knock enemies off the map, eliminating them from play. While this does kill enemies immediately (unless the enemy is confined to an item that prevents them from being O.B.ed), the character does not gain experience from this kill, and most of the time, all non-O.B.ed characters level up as a result of this. All of these rules also apply to the player and items, meaning that a a character will stop receiving benefits from an item if said item is O.B.ed.
Some characters learn abilities by leveling up, but most abilities are learned through fusion. Both characters and weapons gain Mana Points by battling, and these Mana Points can be spent either on earning new abilities for weapons or fusing weapons to characters. (This is not the only combination; weapons can be fused to other weapons, and items can be fused to other items, but characters gain abilities when they are fused with weapons.) The amount of Mana necessary changes depending on how many and which abilities are added during fusion. In addition, characters can only have a set amount of abilities at any given time (both active and passive), meaning it is best to fuse abilities both to a character and a powerful weapon. Abilities are strengthened through repeated use of either that ability or another one in the same category; while this implies a certain degree of character customization, most characters are designed to use only certain types of abilities, all other categories coming at a significantly lower level than their intended ones.
On Marona's island, it is possible to create a large amount of characters. Most of the classes are unlocked by beating them in combat, but other, more specific characters are unlocked through special circumstances (beating the game, reaching the top of the island, etc.). After choosing the class, the player is allowed to give the character a name and a set amount of points to distribute among their stats.
In addition to combat specialties, many characters have special abilities for use outside battle. Merchants sell items, grannies remove Dark Points (status affecting points gained by killing off fellow party members), Titlists add status-affecting titles to characters/items/dungeons, Dungeon Monks create randomly generated dungeons and allow players to play through them, etc.
The story of Phantom Brave: We Meet Again is divided into two parts: the main story from the original Phantom Brave, and Another Marona, a side story available from the start. The latter mode assumes that the player has already played Phantom Brave, meaning it lacks tutorials and is generally more difficult than Phantom Brave, under similar circumstances.
Eight years before the game starts, a group of warriors find themselves fighting a monster named Sulfur. They defeat the monster, but all die in the process. One of the warriors (Jazemine) tries to revive all of them, but only has enough energy to bring one soldier back to life. Two of them ask their Chroma (a mercenary who fights monsters for pay), Ash, the soldier who survives, to look after their daughter, Marona, before they all die. Ash promises, and is able to fulfill this by becoming a Phantom.
Marona spends her time as a Chroma, killing monsters to pay for her island. However, she finds it hard to receive pay, for several reasons. First, Chroma Oxides (bounty hunters opposed to Chromas), like Walnut, steal her jobs, preventing her from getting paid. Second, because she can speak to and summon Phantoms, she is maligned all across Ivoire; everybody calls her The Possessed, and her clients often cheat her out of money, or outright refuse to pay her. In fact, a lot of the mail she receives is hate mail that Ash hides for her own benefit. However, by the end of the first chapter, she manages to take enough jobs to pay for her island entirely. Some of the jobs she takes include defending a family from nearby monsters, retrieving a Rainbow Phoenix, and defeating somebody imitating Raphael the Invincible. (Raphael the Invincible is one of the warriors who beat Sulfur before Ash's attempt, 30 years before the events of the game.)
After gaining ownership of the island, Marona continues to do jobs for people. Eventually, it becomes clear that Sulfur is returning again, as more monsters start appearing and the seals keeping Sulfur out of Ivoire start weakening. However, one of Marona's friends discovers that Putty, a local animal, have the ability to transport objects to other dimensions; she reasons that with enough Putty, they can seal Sulfur back in his world. This plan in mind, Marona, along with her friend and several warriors she met throughout the game (some who sealed Sulfur away 30 years before the game), set out to the Isle of Evil, where Sulfur arrives. When they try to seal Sulfur away, they fail, and he possesses one of the warriors in an attempt to defeat the others. After a long battle, Marona and her friends win.
The story starts with every character in the world mysteriously dying. Oddly enough, Marona is the only character who seems to be alive. Several warriors find themselves on Marona's island, where they find out that they have become Phantoms. In searching for the answer as to why everybody is dead and the world is populated by monsters, Marona stumbles upon an alternate universe version of herself, along with a mushroom being who claims to be God. He also claims that he has the ability to revive the dead, but only those who have been dead for less than two weeks, explaining why Ash, who has been dead for eight years, cannot be revived like the other characters.
This alternate Marona (whom the characters call Carona (a clone of Marona) warns everybody that Sulfur is returning soon, and that in their current state, they are too weak to battle him. If they do defeat him, however, God promises to revive all the people who died in the sudden cataclysmic event at the beginning of the game. Carona spends the remaining time leading up to the battle with Sulfur training them on various islands and revealing details about her life in the process. When the time finally comes to battle Sulfur, the group wins too easily. This is when several plot twists are revealed:
- The Sulfur they were facing was actually a weakened version of the real one.
- God is actually the Merchant of Death, a godlike being who collects deadly weapons for his own uses, and that his goal was to obtain the essence of Sulfur through Carona.
- Marona had been dead the entire game, and Carona had been confining her to keep her from knowing.
Although they eventually run out of time for the revive spell to work, Marona, Carona, and all the Phantoms manage to defeat both Sulfur and the Merchant of Death, reviving everybody in the world in the process. Afterward, Carona returns to her world.