Brain is a antagonist of Fairy Tail.
Oración Seis arc[]
In the battle against the Allied Forces (an alliance consisting of the Fairy Tail, Blue Pegasus, Lamia Scale and Cait Shelter Guilds), Brain doesn't take part, and instead orders the other members of the Oración Seis to finish them off. Once the Allied Forces is finished, Brain moves to eradicate them with his Dark Rondo, but stops upon seeing Wendy Marvell, looking at her with total shock.
After his shock subsides, Brain captures Wendy, and, by extension, Happy, who has latched on to her, and fires his previously halted spell at the Allied Forces before, ultimately, leaving the battlefield. However, unbeknownst to him, Jura Neekis arrives and saves the Allied Forces from the deathly blast. Brain then takes Wendy and Happy back to the Oración Seis' base and informs the other Oración Seis members of Wendy's powerful Healing Magic. He then has Racer bring in a coffin while the others continue to look for Nirvana.
An hour later, Racer returns with the coffin and opens it, revealing a comatose Jellal Fernandes to be inside. Brain then explains to Wendy that he wishes for her to revive him, as he could easily lead the way to Nirvana, and that Wendy, who knows Jellal, owes a debt to him as well. When Wendy hesitates, Brain grants her five minutes to make a decision regarding the matter. Ultimately she chooses to revive Jellal much to Brain's delight. However, immediately upon being awakened, Jellal attacks Brain, sending him plummeting to the lowest depths of his hideout. Scared that Jellal might be intent on taking Nirvana for himself, Brain orders Cobra to follow Jellal, hoping that the man will lead them to the great Magic they seek.
After Racer loses his battle against Gray Fullbuster and Lyon Vastia, Brain wakes Midnight, and orders his adoptive son to kill the Allied Forces. As he continues to look for Nirvana, he senses that Angel has been defeated and vows to not let their sacrifices be in vain. Brain eventually arrives at Nirvana's location, where he is informed, by a frantic Cobra, that Jellal has placed a Self-Destruction Spell on the Magic. Brain, however, shows no worry over the matter, and easily cancels the spell's activation, revealing himself to have created the Self-Destruction Spell. Proclaiming that Nirvana is now his, Brain activates Nirvana's second stage, and declares that the Allied Forces' strongest weapons, "trust" and "unity", are now useless before him. Upon seeing Natsu reach the control center of Nirvana, Brain orders Cobra to defeat him, however, Natsu defeats Cobra in their midair battle.
Cobra returns to his feet, but before he can kill Natsu, Brain attacks him from behind, blasting a hole through his shoulder, heavily wounding the Poison Dragon Slayer. Surprised by this betrayal, Cobra listens to Brain's heart, where he hears Brain think that the Oración Seis are pitiful for having lost to a "common guild". When Natsu asks Brain why he would attack a fellow comrade, Brain answers that with Nirvana, he can simply create a new Oración Seis. Brain then grabs the weakened and helpless Natsu, claiming that he will be the first of his new Six Prayers. However, as he drags Natsu to the control center, he runs into Lucy Heartfilia, Gray Fullbuster, and later Jura. Power-mad, Brain states that with Nirvana, nobody can defeat him, and that he plans to start his tirade by destroying Cait Shelter, but Jura attacks him, knocking him into several nearby stone structures, proclaiming that he won't let Brain rest until he divulges the reason as to why he's aiming to destroy Cait Shelter.
Brain is easily defeated by Jura, but, even though he has fallen, Nirvana remains en-route to Cait Shelter. Brain then pretends to be Hoteye and sends a telepathic message to the group, saying that Midnight is in the room below the King's Room, and that if he is defeated, Nirvana will be stopped. However, unbeknownst to them, Midnight has actually encountered Jellal and Erza, and that the room under the King's Room is actually a trap set up by Brain. When they reach the location in question, they are, unfortunately, too late in realizing that they were tricked, and are caught in a large explosion.
When Midnight is defeated by Erza, it is revealed by Klodoa that all the Oración Seis members are "keys" that keep Brain's other personality locked away. However, now that they have all been defeated, and thus all the seals have been unlocked, this new, chaos-loving personality, Zero has been released. When he arrives at Natsu, Gray, Lucy, and Happy's location, he quickly defeats them, and ceaselessly attacks them afterward. Shortly thereafter, Nirvana finally arrives at Cait Shelter. Klodoa states that the destruction of the guild will make sure Nirvana cannot be resealed; however, Zero shouts that such a reason is meaningless: he needs no reason to destroy. He then orders Nirvana to fire. However the shot is diverted due to the Magic Bomber: Christina hitting one of Nirvana's legs. Aboard the Christina, a fatigued Hibiki Lates informs the others of Nirvana's weak points via Archive, but Zero intercepts the message, taunting the group by saying that he also knows where the weak points are, and that he won't let them destroy them.
After the fallen Fairy Tail members rise once more, they are told that there are six Lacrima powering Nirvana, and that they must pick one and destroy them simultaneously. Natsu immediately picks the first Lacrima, which lead him directly to Zero himself. When he arrives, Zero asks Natsu what business he has, and Natsu states that he is going to destroy the Dark Guild Master. Upon beginning to fight, Zero explains that he isn't the same as Brain, however, he compliments Natsu, whom he states is fighting magnificently for someone of his injured status. Zero then repeatedly whips Natsu with Dark Capriccio, that is, until Jellal Fernandes arrives and attacks Natsu with a large amount of fire.
Zero deduces that Jellal's memories have returned, however, he finds it strange that, despite Jellal knowing of Natsu's non-weakness to Fire Magic, he used it on him anyway; Zero realizes that Jellal did not remember anything. Annoyed by Natsu's bickering, Zero states that the two should fight elsewhere, as they are annoying him, and then proceeds to attack them both with Dark Capriccio. However, Jellal uses his body as a shield, protecting Natsu from the spell. Natsu then accepts the Flame of Rebuke from Jellal, to which Zero states that by doing so, he accepts Jellal's sins as well. He replies back by saying that Fairy Tail is no stranger to sins, and that the real sins are to ignore and stop believing in others. The two resume their battle, but a look of fear appears on his face when he realizes that Natsu has entered Dragon Force. Zero then recalls that Dragon Force is similar to something a real Dragon possesses - the power to utterly destroy everything.
However, the word "destroy" rekindles Zero's confidence, and he attacks Natsu relentlessly, pressuring him, stating that the Fire Dragon Slayer hasn't learned how to properly utilize the power he was gifted with. Disappointed, Zero mentions that the Dragons' power once ruled the ancient world and questions if the power he is currently facing is the same as the one fabled of in legend. Zero then proceeds to deride Natsu, stating that he can't defeat him by himself. Natsu answers back by saying that he can feel his friends supporting him, and that he can feel their strength pouring into him. Zero states that he has had enough, and finds it a pity that he must kill Natsu.
However, Zero mentions that he enjoyed their battle, and resolves to use his strongest spell against Natsu; Natsu and Zero attack each other with Crimson Lotus: Exploding Flame Blade and Genesis Zero, respectively. Zero's spell overwhelms Natsu's, and, by extension, the Fire Dragon Slayer itself, however, Natsu manages to pierce through, simultaneously burning and nullifying Zero's spell. Zero is then rendered helpless by Natsu's Dragon Slayer Magic, receiving the full brunt of Natsu's Crimson Lotus: Phoenix Blade; Zero is thrust into the Lacrima he was guarding, destroying it, as well as knocking him completely unconscious, just as the other five members of the Allied Forces do the same to their own respective Lacrima. With Nirvana deactivated and the Oración Seis defeated, Zero is stopped once and for all.
Tartaros arc[]
Brain is seen released, along with the rest of Oración Seis, due to Cobra's actions. As he is congratulating him and proclaiming the return of his guild, Cobra brutally strikes him down, to which none of the other members of Oración Seis seem to contest after having learned they were being used by Brain. Afterwards, he is seen laying on the ground dead with Midnight towering above him. While he is in this state, the rest of the Oración Seis begin battling against Jellal. When he begins overpowering them, striking them down one after another, Brain, still lying on the ground, smirks as the seals on his face start disappearing.
With Zero quickly awakening, the alternate persona rises and screams to Jellal that he is the one that is going to disappear, a response based around the man's comment that he is going to defeat them all; Zero quickly and gleefully fires a Dark Capriccio at Jellal that pierces the man's abdomen. With Jellal mortally wounded, Zero pounces on the man and violently punches him, sending blood spattering. Maliciously laughing, Zero shouts that his final punch marks Jellal's end. However, it is soon revealed that Midnight created an illusion, and that Brain is in fact still on the ground, dead.