Sora runs ahead of Goofy and Donald as they chase after Pluto to get the letter with the Mickey-head seal on it. As he runs he realizes that he no longer hears Goofy and Donald and turns to see why they stooped running after Pluto. But Donald and Goofy are gone, as he turns to see if Pluto is still there the world goes dark around him. He wakes up in Traverse Town.
Goofy and Donald find themselves in Disney Kingdom once more. But as they try to leave to find Sora again they encounter a barrier that will not allow them to leave in another Gummi Ship. So, for the time being they are forced to remain in Disney Kingdom.
When Kairi arrived back on Destiny Islands she told Tidus, Selphie and Wakka what happened. They wait for Sora and Riku to return but as weeks pass by Kairi dreams of Sora and Riku in need of help, being killed, fighting heartless and losing themselves to the darkness each night since she has returned to Destiny Islands. One day she enters the Secret Place to look at the drawing on the wall of Sora and herself and finds the door is open. She runs to get the others and tell them that the door has opened and as she does she sees the shooting stars in the sky, the sign of a gate to another world collapsing or another world is taken by the darkness. Tidus decides that if the door is open then they should go find Sora and Riku because the door being open must mean something and with Kairi's dreams of the two missing boys it must mean they need their help. They pack bags and walk through the door together. The door takes them to Hallow Bastion.
The ones at Hallow Bastion began going through the books in the library and Ansem’s reports. Aerith went into Ansem’s private study and found what looked to be his journal. In the journal were details about his daughter and his plan to send her out into the universe to find the Key Bearer. She also learns that the door of darkness and the door of light must be opened to go to the world in-between, where they believe they have to go to stop all heartless. But only once every world is locked and the Princesses are gathered together will the path leading to the door be revealed.
Riku was with Mickey for a time in Kingdom Hearts but lost him when he found the way into the In-Between world. Now he travels alone acting as one of the Unknowns. There are NEO Heartless and the Unknowns only there. Time flows differently there, a bit like the land of summoned monsters. The Unknowns are protecting something as well trying to find a way to theirs souls. If you have a soul you can travel between the worlds but Riku does not know this.
When Ansem was destroyed in Riku's body he went into the In-Between world. He discovered he could move between all the worlds and has gathered up those that wish to rule/destory their worlds and those powerful enough to help him. The Heartless remain under his command. He has someone to create different heartless.
Kingdom Hearts: The place where light once was but now is darkness. Now this is the World In-Between. ('Long ago, people lived in peace, bathed in the warmth of light. Everyone loved the light. Then people began to fight over it. They wanted to keep it for themselves. And darkness was born in their hearts. The darkness spread, swallowing the light and many people's hearts. It covered everything, and the world disappeared. But small fragments of light survived...in the hearts of children. With these fragments of light, children rebuilt the lost world. It's the world we live in now. But the true light sleeps, deep within the darkness. That's why the worlds are still scattered, divided from each other. But someday, a door to the innermost darkness will open. And the true light will return. So, listen, child. Even in the deepest darkness, there will always be a light to guide you. Believe in the light, and the darkness will never defeat you. Your heart will shine with its power and push the darkness away. Do you understand, Kairi?')
Dual Keyblade Wielding Unknown = Sora
Blindfold Unknown = Riku (The blindfold is there so the appearance of the Unknowns don't cloud his judgment and he might not want the Unknowns to realize he has a soul.)
Unknown Sitting On Rock = Kairi
Big-Eared Unknown = Mickey
Unknown Who Walks Through Stone = Ansem (Has a soul?)