After her near second demise, Maleficent became bitterly enraged, tormented by her internal hatred for Sora. The boy, though not even a full-fledged keyblade master, has bested her, defeated her minions, crushed her villanous allies, and killed her. Her demented desire for Kingdom Hearts is put on hold, as she vows to kill the "fool that made the mistress of all evil a mockery!"
Birth by Sleep
"Imagine with me, the most glorious of futures... Seven of the purest hearts, each overflowing with light. When brought together, they grant the power to rule all worlds."
—Maleficent to Terra
Maleficent appears in Kingdom Hearts: Birth By Sleep, her role downgraded to that of a minor antagonist, only appearing in her home world of Enchanted Dominion. At some point in time,Master Xehanort made contact with her and enlisted her help in luring Terra to darkness and told her about Kingdom Hearts and the seven Princesses of Heart. From this point on, Maleficent became even more power hungry and lusted to gain complete control over all worlds, not knowing she is simply being used by Master Xehanort as part of a much bigger plot that would unfold in the following decade.
At her home world, Enchanted Dominion, she mostly plays out the same role as in the original movie, only this time manipulating the darkness in Terra's heart to force him into stealing Aurora's heart in return for helping him locate Master Xehanort. She offers Terra the opportunity to join her in her quest to rule the worlds, but he flatly refuses. Later, Ventus visits the world and frees Aurora's heart, inciting Maleficent's fury. In the ensuing fight, Ventus defeats Maleficent, who reveals that it was Terra who stole Aurora's heart. Aqua arrives and staunchly denies it, as does Ventus, although he seems unsure as what to believe. After Aqua refuses Maleficent's offer to join her in Terra's place, Maleficent throws her into the castle dungeon with Prince Phillip, whom Maleficent had captured earlier to stop him from awakening Aurora. Aqua and Phillip break out of the dungeon with help from Flora, Fauna and Merryweather and make their way towards King Stefan's castle to wake Aurora. Maleficent gives chase and confronts them on the bridge to the castle, transforming into a dragon to battle them directly, but is defeated. Before she can be finished off, Maleficent flees the scene and begins her plans to capture all the seven princesses. Later on in the game, she crosses paths with the imprisoned Pete, and frees him, setting the scene for their alliance.
A year after the events of Birth by Sleep, the Heartless soon appeared and Maleficent decided to use her immense power of darkness to control the creatures and build up a destructive force to aid her in her plans to conquer all worlds. Over time though, her darkness went beyond her control and the Heartless soon used it to manipulate her for their own ends. She first captures Aurora and destroys her own world, going off to Hollow Bastion to make it her new base of operations.
With the aid of Pete, Maleficent soon became the mastermind behind a council of Disney villains seen in Kingdom Hearts, composed of Hades, Jafar, Ursula, Oogie Boogie, and Captain Hook. Pete, as her then-unseen henchman, had helped assemble this group and was off building an army of Heartless for her to increase their forces. Acting as a guide, Maleficent warned each of her followers that they should be wary of the darkness, ironic as she herself was perhaps the biggest victim to the darkness. She led this group in pursuit of ultimate power by controlling the Heartless and unlocking the Keyhole that leads to Kingdom Hearts, the heart of all worlds.
She used Hollow Bastion, the former home of Ansem the Wise, as a base of operations where she directed the affairs of the group. She used Ansem's report to help her understand and gain further control of the Heartless and recruited Riku, Sora's best friend, to her side. Once she saw that Riku could wield a Keyblade, she used the Darkness in Riku's heart to corrupt him and turn him against his friends.
Maleficent eventually told Riku her plans to find Kingdom Hearts, involving the Princesses of Heart. Maleficent persuaded Riku to go after Kairi, as she is also a Princess. Maleficent lied to Riku and told him that she'd help Kairi regain her heart once she had control of the Kingdom Hearts. She in the meantime convinced Riku to commit sinister actions, such as abducting several of the Princess of Heart, gave him the power to control the Heartless, and even ordered him to attempt to murder those who interfered in her plans. Riku, blinded by his jealously of Sora and lust for power, did as he was told and became more and more corrupt as his heart gave in to the darkness.
While Maleficent's plan seemed to be working, her allies were falling to Sora. With each failure, she would have to make another plan or just ignore it for another time. One by one, each of the Disney villains was defeated by Sora. Maleficent's knowledge and control of the powers of darkness had enabled her to control the Heartless, or so it seemed. Unknown to Maleficent, the Heartless were simply using her to reveal the Keyhole in Hollow Bastion, and in the meantime were eating away at her heart. Overconfident in her abilities and underestimating Sora's, she fought him and lost.
When Riku, possessed by Ansem, Seeker of Darkness, unlocked her heart, the darkness seeped into it, and Maleficent turned into a far more powerful version of her dragon form, but the darkness did not see her through. Although she proved a far more dangerous enemy as an empowered dragon, Sora still defeated her for the second time, the darkness ate her heart and she faded away into darkness.
By defeating Maleficent, Sora obtains the fifth page of Ansem's Report, and Donald learns the Cheer ability. Defeating Dragon Maleficent rewards Sora with the Fireglow Gem, which unlocks the ability to summon Mushu if taken to the Fairy Godmother.
Maleficent is revived in Kingdom Hearts II, in which she poses as a secondary villain but still plots against Sora and the others. Her raven, Diablo, brings her empty robe to Yen Sid's tower, and the memories of Flora, Fauna, and Merryweather accidentally bring her back to life.
In Kingdom Hearts Another Report, it is hinted that Organization XIII is inadvertently responsible for her return. Xemnas once sent Axel and Roxas to Hollow Bastion to wipe out Heartless and release a raven from a cage suspended from the ceiling. It is heavily suggested that this raven is Diablo and was released to revive Maleficent. The Organization may have planned to use her to create more Heartless for their plans. Like in Kingdom Hearts, she attempts to control the Heartless to locate Kingdom Hearts. However, she now competes with Organization XIII for supreme power and considers the group and Nobodies in general as vastly inferior to her and her Heartless, even as far as calling them "white husks".
Maleficent, with the help of her only loyal follower remaining, Pete, goes from world to world reviving her other followers and building an army of Heartless. Although only Oogie Boogie is witnessed being revived, it may be guessed that she is also responsible for the return of Ursula and for Barbossa, Scar, Hades, and Jafar using Heartless. Indeed, when she first meets up with Pete again, she asks about "the others," suggesting she was supposed to be holding a meeting with "them" like she did in the original game. Pete, however claims that "they must have had something better to do," perhaps meaning he was busy with his own endeavors. This infuriated her, and she demanded from Pete what could be more important than her return.
Maleficent reveals herself to Sora and his friends at Disney Castle when she tries to fill the Hall of the Cornerstone with Darkness in order to take over the Castle and make her new base of operations, worrying Queen Minnie. Maleficent is defeated however by Sora when he and his friends go back in time and stop Pete from destroying the Cornerstone of Light. Maleficent appears in Halloween Town and tries to destroy Christmas town by resurrecting Oogie Boogie but his memory loss causes him to drive her away and Sora defeats Oogie Boogie. She then appears in Hollow Bastion during its invasion by Heartless. This is the turning point in the game, where she and the Disney villains finally lose control of the Heartless to Organization XIII. At the climax of the battle she holds off the Nobodies so that Sora may escape and devise a way to defeat Organization XIII. Although she hated Sora, she realized that she couldn't defeat them herself, since they easily defeated her Heartless, and even took control of them from her. She flees a battle against Saïx, escaping with her life, bringing Sora to the Realm of Darkness.
She last appears in The World That Never Was in one more attempt to acquire a suitable headquarters, aiding Sora once more by fending off an immense wave of Heartless with the help of Pete while Sora defeats Xemnas, though she claims that she will take the castle for her own afterwards. The outcome of this is unknown.
"Drag all that you see into deepest darkness!"
—Maleficent to the Shadows attacking Data-Sora
Having apparently survived the destruction of The Castle that Never Was, Maleficent was at a loss with her plans with the Heartless gone, her control over the darkness weakened, all her allies save for Pete defeated, and still without a base of operations. Desperate to make yet another comeback, the sorceress sent Pete to Disney Castle to spy on the king and bring her up to date on events. Pete eventually entered the journal world when Mickey turned the journal into a Data World to find answers to unsolved questions. Maleficent was summoned into the data world by Pete when he was sent there.
Together they decided that they could use the data world to forward Maleficent's original plans to find Kingdom Hearts and fill the worlds with darkness. The pair planned to build up a huge army of Heartless under their complete control by using the Journal's data on the creatures and then send them into the real world to conquer Disney Castle and the rest of the worlds. Maleficent planned to either destroy Mickey or simply leave him trapped in the Journal's data world.
She reappears in person in the data version of Agrabah. At the entrance to the Cave of Wonders, she strikes down the data version of Sora and destroys his data Keyblade. After, she gloats and summons Shadows. Data-Sora later fights and defeats her in her Dragon form. Later, when the debugging of the journal is complete and the Data World is being deleted, Jiminy Cricket remembers that Pete and Maleficent never left the Data World. Data-Sora rushes back to the Data Hollow Bastion to save them, and finds them fighting the corrupted version of Sora's Heartless, who is completely immune to their attacks. The Data-Sora attempts to save them, but they are both deleted before he can do anything.
However, after the battle, Data-Sora and King Mickey walk outside to find them alive, standing next to Data-Riku, who explains that there was a "rift in the data" where he was able to rescue them. Maleficent points out that this makes them even, referring to when she helped them in Kingdom Hearts II. Data-Riku then escorts Pete and Maleficent out of the Data World. A digital version of both later appear when Data-Sora goes to Castle Oblivion and attack him before leaving.