The Villains are a group of scoundrels from various worlds who seek to harness the power of the Heartless. They are led by Maleficent, and originally had the goal of capturing the seven Princesses of Heart and taking control of Kingdom Hearts, to rule all worlds. After their first defeat at the hands of Sora, they are much less organized, and while they occasionally cooperate on a one-on-one basis, they no longer work in concert and follow their own goals.
Each Villain is usually the boss battle for their native world.
The track "Villains of a Sort" serves as the group's theme and is used for most cutscenes involving the Villains. However, it is also used for a few other Disney villains that are unaffiliated with Maleficent's group, such as The Queen, Shan-Yu, and Gaston.
Kingdom Hearts Birth by Sleep
Maleficent was contacted by Master Xehanort at some point before Terra, Aqua, and Ventus left the Land of Departure. He told her about other worlds, the Princesses of Heart, and Kingdom Hearts, explaining how they could be used to rule all worlds. Identifying Aurora as a Princess of Heart, Xehanort takes her heart for Maleficent on the condition she tricks Terra into thinking he had taken it. However, Aurora was saved by the combined efforts of Ventus, Aqua, and Prince Phillip.
Realizing the search for the Princesses would take a while, Maleficent resolves to gather others to help. Finding Pete, who had been banished to another dimension by Queen Minnie, she decides to free him and make him an ally.
Future members of the Villain alliance also appear in their respective worlds. Captain Hook is put in his place by Terra and Ventus, while Hades attempt to recruit a "Dark Warrior" to do his bidding is foiled by Terra and Aqua.
Between Kingdom Hearts Birth By Sleep and Kingdom Hearts
Maleficent spends the next decade gathering potential allies to aid her in their search for the Princesses of Heart. She eventually recruits Captain Hook, Ursula, Hades, Oogie Boogie, and Jafar. The group also learns about the power of the Heartless and use them as minions in their quest. However, while the group was aware of the dangers posed by using the Heartless, they failed to realize they were just puppets of the Heartless who only obeyed them in an attempt to gain control of Kingdom Hearts.
They gathered ten of the thirteen Ansem's Report,making use of the Heartless Manufactory in the basement lab of Hollow Bastion to create custom Heartless for unique worlds and command lesser Heartless for them.pages of
The Villains have two main goals: find the Princesses of Heart and send the Heartless into the Keyholes of many worlds, destroying them in the process. Using the Heartless, the group makes Hollow Bastion their base and successfully imprisons Aurora, Belle, Cinderella, and Snow White there while destroying their Worlds.
Countless worlds have fallen in their quest for the Princesses of Heart. After the destruction of Destiny Islands, Riku ends up on Hollow Bastion, where Maleficent takes him in. The Villains send Guard Armor to Traverse Town to draw out the Keyblade wielder. After discovering Sora, the Villains keep an eye on him; unfortunately, he begins sealing keyholes to keep the worlds safe from destruction. After Clayton became a puppet of the Heartless, they watch him perish.
To turn Riku against Sora, Maleficent takes him to Traverse Town to see him with his new friends. With Riku bitter, Maleficent promises to help him find Kairi if he helps the Villains. While Jafar is defeated, Riku kidnaps Jasmine; Maleficent rewards him by having Hook take him to find Kairi. Riku appears in Monstro, planning to kidnap Pinocchio to find a way to restore Kairi's heart.
After Ursula and Oogie Boogie fall to Sora as well, Captain Hook kidnaps Wendy under the assumption she's the last princess of heart. However, Riku informs him that she is not and takes Kairi to Hollow Bastion. Hook is soon defeated and Hades loses interest in the plan.
While Riku keeps Sora busy, Maleficent attempts to open the Final Keyhole with six of the princesses' hearts; however, as Kairi does not have her own, the keyhole remains in an unstable limbo. Ansem, Seeker of Darkness possesses Riku and uses the six hearts to create a Keyblade of heart, which he uses to unlock Maleficent's heart, leading to her defeat and heart traveling into the past. With the Villains out of the way, Ansem takes over their plan and tricks Sora into helping him finish the keyhole.
Elsewhere, Pete is busy searching for ways to create powerful Heartless , but remained unaware of Maleficent's demise.
Kingdom Hearts 358/2 Days
With Sora dismantling the Villains organization previously, Hades and Captain Hook have lost interest in universal domination and have re-focused on their worlds alone. Pete, unaware of the loss of his group, continues his mission to create powerful Heartless.
Pete searches Agrabah, shortly after the Antlion-induced sandstorms end, to find the Cave of Wonders; inside is Jafar's lamp. He encounters Roxas and Xion when they investigate the cave, believing they want the lamp and attacks. Their scuffle causes a cave-in, scaring off Pete.
Captain Hook comes across treasure maps, which only lead him to buried junk and Heartless. Unknown to him, the maps are fakes created by Pete, who is trying to create a powerful Heartless from his greed. After the defeat of Ruler of the Sky, Pete realizes how much the Organization is interfering with the Villains' plans.
Kingdom Hearts Chain of Memories
Sora and Riku's respective memories of Hades, Jafar, Oogie Boogie, Ursula, Captain Hook, and Maleficent are given life within the recreations of their respective worlds. When Sora encounters them, they are involved with plots that deal with memory, either directly or indirectly. DiZ tampers with the recreations he gives to Riku, so that only the Villains and boss Heartless like Trickmaster and Parasite Cage appear. 
The machinations of the Villains, along with their failure and respective fates are known to the Organization. Only Maleficent is specifically mentioned in conversation, due to the brief presence of her copy that was slain by Riku.
Kingdom Hearts II
The Villains are properly reorganized with Maleficent's return; however, the group has been reduced to just her and Pete.
Pete attempts to bring Hades back into the fold, but he is more focused on defeating Hercules. Having failed to find Jafar's lamp, along with Oogie and Ursula gone, Pete returns to Maleficent without any additional allies.  After Pete explains the numerous setbacks to the Villains caused by Sora and the Organization, a furious Maleficent dismisses him. However, she quickly takes him back when he conjures a portal to the past. They attempt to turn Disney Castle into the Villains' new base by destroying the Cornerstone of Light in the past, but Sora seals their portal.
Undeterred, they attempt to rebuild their forces by recruiting new members like Barbossa and Scar, while trying to turn Jafar into a Heartless and bring back Oogie Boogie. However, Barbossa, Oogie, and Scar meet their demise, and Jafar is sealed away, leaving the Villains a duo.
Maleficent and Pete launch a full-scale war to retake Hollow Bastion castle after the MCP causes some destruction. However, the Organization sends Nobodies to swat them back. Pete flees, while Maleficent confronts Saïx on the Organization's claim on Kingdom Hearts; however, she forced to retreat when Dusks overpower her. The Organization takes control of the Heartless from the Villains, ending the battle.
Maleficent and Pete break into The Castle That Never Was, intending to make it their new base. After Sora's team take down Xigbar, Luxord, and Saïx, a swarm of Heartless attack the castle, attracted by the heart shower from the broken Kingdom Hearts. Maleficent and Pete offer to take care of the Heartless if they destroy Xemnas; they would take the castle afterward.
Kingdom Hearts coded
Having abandoned the idea of taking The Castle That Never Was, Maleficent decides to have Pete spy on Disney Castle to find out what the King is up to. Pete gets sucked into the datascape, calling Maleficent in after him. Despite not understanding the artificial nature of the world, Maleficent decides they can use the Heartless data to amass an army to send back out in Disney Castle to begin their conquest of the worlds. However, the Villains are thwarted by Data-Sora and escorted out by Data-Riku. Maleficent realizes their misadventure reminded her of the Book of Prophecies; she decides that the datascape may hold a connection.
Data versions of Hades and Jafar appear in their respective worlds. Hades takes advantage of the Blox warping his world into a labyrinth, sending Cloud after Hercules, but both team up with Data-Sora to slay Cerberus, the source of the Blox and knock Hades for a loop. Jafar is granted a copy of Genie's lamp by the real Pete, granting him unlimited power. However, Data-Sora traps him inside the very lamp that empowered him.
Kingdom Hearts Dream Drop Distance
Taking advantage of the King, Donald, and Goofy's absence from Disney Castle to oversee the Mark of Mastery Exam at Yen Sid's tower, Maleficent takes Queen Minnie hostage. She sends Minnie's crown with her raven, Diablo, along with a letter demanding the King return.
During a standoff in the library, Maleficent reveals Xehanort once told her of other worlds and the seven hearts of pure light that would enable her to rule them. However, due to the complexity of the worlds, Maleficent decides to take a different approach, using the worlds' data; Pete explains they want the datascape. When Mickey refuses to yield, she attempts to attack him with her magic. However, the magical flames are blocked by one of Lea's Chakrams, while the other surprises Pete and allows Minnie to escape. With her hostage gone, Maleficent declares she will take the data someday before retreating with Pete.
Kingdom Hearts III
Maleficent and Pete begin searching for the Black Box, which she believes holds the Book of Prophecies. Their search brings them to Olympus, where a miffed Hades tells them he no longer wants to be part of the Villains. However, he does direct them to Pandora's Box buried in Thebes' garden, believing it to be the box they're after; however, it's not."
Concluding that the Real Organization XIII must also be looking for the Black Box, Maleficent and Pete begin following them around the worlds.  Getting spotted in San Fransokyo, Maleficent pays no mind to Dark Riku's warnings about overstepping her bounds and getting consumed by darkness again. The eve of the next Keyblade War, Maleficent decides to end the search; the box does not exist, yet.
Notes and references