The protagonist of Phantom Brave is a 13 year old girl named Marona. Having lost her parents at a young age, Marona lives on Phantom Isle in the land of Ivoire with a phantom named Ash. While he was still alive, Ash worked alongside Jasmine and Haze (Marona's parents) as a Chroma, a sort of bounty hunter. On an assignment at the Isle of Evil, a fragment of a malevolent being known as Sulphur attacked the group, mortally wounding them. Using the last of his life energy, Haze attempted to revive Ash after the battle. However, there was only enough life left in him to bring Ash back as a phantom. Haze and Jasmine's dying wish was for Ash to watch over their then-infant daughter Marona.
Marona is the only one able to see Ash in phantom form. This is primarily because of her unique ability known as Chartreuse Gale. This ability not only allows her to see and interact with phantoms, but temporarily bind their souls to objects and give them a temporary body using a skill called "Confine". Using this, she can summon Ash and other phantoms of her creation to the world of the living to aid her in her own endeavors as a Chroma, similar to the work done by her late parents. This work is very difficult for Marona, though. Because she possesses the Chartreuse, many assume that she is controlled by evil spirits and are afraid to even interact with her, much less employ her for Chroma work. Also, in the early portions of the story, people who offer Marona employment would rescind any rewards upon completion once they discover that she has the Chartreuse ability.
As she continued her Chroma work, Marona's path eventually crossed with a man named Walnut. Walnut prided himself on his status as a Chroma Oxide, one who secretly follows a Chroma on his mission and steals the reward for the work. Walnut regularly tries to meddle in Chroma-related matters involving Marona, but is rarely successful. As they continued their work, Ash and Marona also met a sickly young girl named Castille. Confined to a bed and a wheelchair for most of her life, Castille was unable to go out into the world or make friends. However, after helping Castille's family on an assignment, Marona agrees to be her friend, and leaves behind a Putty, a mischievous spirit found on an earlier assignment, to keep Castille company.
More time passes, and signs of Sulphur returning to Ivoire in full force are more apparent. Earthquakes increased in frequency and monsters plagued the land, with a lesser form of Sulphur known as Wraith appearing to attack Ash and Marona several times. Ash and Marona meet more people who are aware of these signs and are making preparations to battle Sulphur, if necessary. Among these individuals are Raphael, a knight from a legion known as the Nine Swords of Ivoire, and Sprout, a renegade soldier whose family was killed by Sulphur when he attacked many years earlier. Sprout seems to side with Ash in this fight, but Sprout is bent on the destruction of Sulphur at all costs, no matter the means used.
As preparations for the final battle are made and Ash and Marona return to the Isle of Evil, Ash and Raphael engage in a duel. Raphael is injured, and entrusts Ash with Heliotrope, his sacred sword, for use in his battle with Sulphur. At the center of the island lies a portal from which Sulphur is fully entering the world, and upon the heroes' arrival to this point, they expect to engage in combat with Sulphur immediately. However, they are intercepted by Sprout. Having gone mad from his own power, Dark Eboreus, Sprout attacks Ash and Marona, and in turn is killed in the battle.
Ash and Marona finally enter battle with Sulphur, and after the fight, Sulphur is weakened, but still making an effort to enter into Ivoire. At that point, Walnut appears, and sacrifices his own life to close the seal between Ivoire and Sulphur's domain.
Unlike most tactical role-playing games, whose game board contains a grid used for movement, Phantom Brave has a gridless system, in which each character can move a certain number of dm (decimeters) in each turn. The terrain also has traction and bounciness characteristics, which affect how long characters continue to slide along after they stop moving and how high they bounce when they jump down from a ledge. On slippery surfaces, it's possible to make the characters "ice skate" by moving very short distances (consuming few dm) and letting them slide to their destination.
Also unlike most TRPGs, the board does not have barriers on the edges. Combined with the hold and throw system inherited from Disgaea: Hour of Darkness, characters can be thrown or hit off the field and sent O.B. (out-of-bounds). O.B.'d characters are gone for the rest of the map. When an enemy is O.B'd, the levels of the remaining enemies rise, so the player can trade many small problems for one large one (the last enemy on the map cannot be thrown O.B.).
Another unique feature for character development is the fusion system. All characters and weapons accumulate mana whenever they kill an enemy. This mana can be spent to fuse two characters together, an item to a character, or an item to an item. Fusion increases the level cap of the beneficiary by the level of the consumed item or character. By spending mana, the player can improve equipment percentages (stat bonuses given to characters who equip the item or character) and confine percentages (bonuses to characters confined in the item on the field), and transfer skills to the beneficiary. In Phantom Brave, weapons have a much greater effect on stats than the characters, so mastering the fusion system to create super-powerful weapons is essential to conquering the extra maps. Also unlike most CRPGs the max level is 9999. However, this ceiling level seems to be a common motif in games by Nippon Ichi Software.
The random dungeons from Disgaea's Item World return in Phantom Brave. They are no longer associated with items, and are simply known as Random Dungeons. While on Phantom Isle, a Dungeon Monk can be asked to create a Random Dungeon. Some characteristics of the dungeon can be seen before creation, including the type and general number of enemies present, the floor conditions, and if the use of equipped weapons is restricted or not. Dungeons also have titles, which are applied to every enemy in the dungeon and change (usually improve) as floors are cleared. These titles can later be removed and placed on player characters. Random Dungeons take the form of a linear series of floors. Unlike in Disgaea, where to descend to the next floor one may merely move a character to a certain panel, in Phantom Brave one must defeat all the enemies present to continue. Occasionally, a floor may have a special named layout (for example, "Self-Styled God" floors have a stronger enemy in the center of a terraced layout). These floors occur randomly and confer an extra bonus upon completion. To leave a random dungeon, one must either clear every floor, or use a Dungeon Monk's Return skill (which costs money proportional to the current depth).
While not in battle, Marona can return to her home - Phantom Island - where she can summon new phantoms to aid her. Phantoms actually populate the island as non-player characters. Many classes have a utility on the island - Merchants sell things, Healers heal and resurrect, Dungeon Monks allow the player to go to random battle fields, and so forth.
As Marona and her group of Phantoms advance through the chapters, her ability to create Phantoms grows. The player starts off by being able to make a small amount of Phantoms, but as time goes on, one will be able to create more powerful Phantoms, such as fenrirs and zombies.
Like Disgaea before it, Phantom Brave has a series of extra maps following the main storyline. These maps feature cameos by some members of the Disgaea cast as enemies; after defeating them, they join the player's side as "phantom doubles". While the first couple of extra maps can be completed immediately after the main story, the later extra maps are very difficult and require a large amount of time to be spent leveling characters and fusing weapons for characters before they can be completed.