While the Union leaders started following their rulebooks, the protagonist dealt with their own issues. During a routine Heartless hunt, they found themselves in a Corridor of Darkness that transported them to a new world — Enchanted Dominion. Here, they ended up taking responsibility for Princess Aurora's safety, which inevitably brought them into conflict with Maleficent. Unbeknownst to them, however, this Maleficent was different from any other Disney villain they've fought so far. She was real.
Kingdom Hearts Union Cross quests 735 through 841 detail a major occurrence that affects the entire Kingdom Hearts timeline. Said occurrence kicks off a series of events that explain how Maleficent returned in Kingdom Hearts 2 and why she's been obsessed with time travel and the Book of Prophecies ever since. This writing will act as an explanation and interpretation of these Kingdom Hearts Union Cross events, so expect spoilers ahead.
Unchained 0 [Zero]
The original X [Chi] browser game contained a patent Kingdom Hearts secret ending called "Unchained 0." The movie plays after players beat the Keyblade War chapter of the story, and it reveals that Maleficent successfully time-traveled to Union Cross' time period. Despite this movie's importance, it didn't appear in Kingdom Hearts Union Cross, not even during the Keyblade War retelling. However, what happens in the film is canon, albeit with some removals, such as the protagonist's scenes.
Darkness
Maleficent can't understand how she lost to Prince Philip a second time. Limping across the catwalk of her castle's highest tower, she broods over how Philip managed to defeat her the same way he did when he teamed up with Master Aqua. Despite Maleficent having knowledge of her first defeat, the second played out exactly the same way, only this time, Philip had help from the protagonist. She can't understand why the past refuses to change for her when she has the obvious advantage.
It's a presence from the shadows of the tower's entrance that answers her question. The entity tells Maleficent that she can refer to them as "Darkness" and that she can't change the past because too many powerful people knew she was coming to try. Too many people knew she wanted to erase her failures, grab the Book of Prophecies, and re-collect the seven Princesses of Heart, so they just laid a trap to stop her from doing any of it.
Time Travel
Time travel only works after fulfilling certain conditions, and the trap plays on these rules. First and foremost, an individual can only travel to a time where a version of them exists. This "version" can be anything: an illusion, a digital recreation — anything. In other words, the person attempting to travel doesn't have to have actually lived in the time they're trying to jump to. If a powerful illusion of them existed during that time, they would be able to travel to it, and nothing casts illusions quite like the Book of Prophecies.
The Book of Prophecies can project illusions based on the future (Sora's time) into Union Cross' time. These illusions are so powerful that they're indistinguishable from their real counterparts. This is why the Foretellers used the Book to conjure the future versions of Disney worlds, as these worlds contained Heartless for the Foreteller's wielders to battle and collect light from. Darkness knows that Maleficent learned all of this from the old Keyblade wielder Master Xehanort and that she tried to capitalize on the knowledge when a Xehanort-possessed Riku exposed her to the second step necessary for time travel.
Kingdom Hearts 1
The second rule of time travel demands that travelers leave their bodies behind and exist only as hearts, as hearts are the only things capable of moving fast enough to break the time-space barrier at light speed. Anything with a body or physical form is unable to pull off such a feat. It doesn't matter how an individual loses their body, so long as their heart exists after the fact. Keyblade Masters are particularly versed in doing this. They can remove their hearts and the hearts of others from their bodies with ease.
When Riku, possessed by Xehanort's Heartless, stabbed Maleficent with the Keyblade of People's Hearts to bring about her full power, he "unlocked" her heart in the process, making it, for all intents and purposes, pilotable without a body. Upon being stabbed, Maleficent remembered Xehanort's teachings, and once Sora destroyed her body, she used the opportunity to jettison her heart to Union Cross' time.
The Trap
Unfortunately for Maleficent, the Master of Masters knew she would try to get to Union Cross' time by targeting an illusion of herself cast by the Book of Prophecies, so the Foretellers just never used the Book to create Enchanted Dominion, her home world. Even if they did, all the worlds created by the Book became inaccessible after the Keyblade War because the Foretellers vanished with it. Therefore, Maleficent never would have made it anyway.
Maleficent can thank the Master and Ava for the fact that she made it so far back at all, as it fell in with their plans. Only Lux — light — can rebuild the real world now that the Keyblade War destroyed it. However, Lux can only be obtained by converting the future's darkness, the Heartless, into light through the Power Bangles given to the Foreteller's wielders. Since the Master and Ava knew the worlds capable of producing Heartless would disappear after the war, they created fail-safes, and within these fail-safes lies Darkness' trap.
The Data World
Every world created by the Book of Prophecies was recorded as data before the war took place. After the war, a select group of wielders, Ava's Dandelions, were sent to this Data World to gather the Lux necessary to rebuild the real one. Since the Master knew Maleficent was coming, Enchanted Dominion was also created in the Data World so that her heart would target her digital recreation, thus trapping her in the digital landscape.
To answer Maleficent's question on why she can't change the past: the data of the Data World is coded to play out events exactly as they happen in the Book of Prophecies. The Book says Maleficent loses to Philip and a Keyblade wielder, so that's what the Data World makes happen. Even if Maleficent could change the outcome in the Data World, it would not affect the recorded history of the real world.
And no, Darkness didn't trap Maleficent here because they fear her power like Maleficent believes. They trapped her because they didn't want her to learn what happened in the home world of the seventh Princess of Heart (Kairi), while she resided there, then take that knowledge back to the future with her. As an extra precaution, the Data World only contains six of the seven worlds housing a Princess. So even if Maleficent could go looking for the seventh, she would never find her as her home world, Radiant Garden, doesn't exist in the Data World.
However, Darkness reassures Maleficent that they can't keep her trapped in the Data World forever; she must return to her own time. Since Darkness' has already stopped Maleficent from doing anything fruitful with her time jump, they're going to send her back to the future. Because of Xehanort, Maleficent thinks traveling back to the future is impossible, but Darkness knows how.
Kingdom Hearts Union Cross is on IOS and Android.