Kingdom Hearts II begins with a boy named Roxas, who has been having a lot of strange dreams about Sora lately. The last few days of Roxas’ summer vacation are winding down, and as the days go on, bizarre things start to happen to him. He discovers a mysterious weapon called the Keyblade, a weapon only he seems to be able to use, not to mention the enigmatic Axel and DiZ fighting over him. Roxas starts to uncover the truth of who he really is when he meets a girl named Namine, who has been working to put Sora’s memories back together. She tells Roxas that he holds half of Sora, and that Sora needs Roxas to be whole again. Roxas tries to meet Sora, but his plans backfire when Axel intervenes. He defeats Axel, and finds Sora, only to have him awaken.
Awake and ready to continue searching for their missing friends, Sora, Donald, and Goofy set out on a new journey. They soon learn that despite their recent efforts in their fight against Ansem, the worlds have fallen into a state of unrest due to the work of the mysterious Organization XIII, a group of new enemies called Nobodies whose true plot remains unknown. And if the Organization wasn’t enough to worry about, a new enemy named Pete is working with Maleficent to muster up an army of Heartless to take over all of the worlds.
Armed with a new outfit and new powers, Sora and his friends travel to many worlds, new and old, in search of Riku and the King, and any news they can gather on this mysterious Organization XIII. Meanwhile, Axel travels to the Destiny Islands and chases Kairi through a dark portal to Twilight Town. Sora soon learns that the Organization is keeping Kairi captive and so he sets out to rescue her in addition to finding his friends.
Upon the gang’s second trip to Hollow Bastion, they learn that the Ansem they fought during their previous adventure was actually the Heartless of the real Ansem’s apprentice. They also learn the Organization’s true goal, as well as meet the leader of the Organization, Xemnas, the Nobody of Ansem’s number one apprentice, Xehanort. Sora also learns that the Heartless he’s been defeating with the Keyblade are only helping the Organization reach their goal even faster. Faced with no other option, he continues to fight the Organization and the Heartless as he journeys to find his friends.
The trio eventually find a way into the Organization’s stronghold and decide to storm the castle. Upon making his way to the castle, Sora encounters a strange young man in a black coat. After a quick fight, the man in the black coat surrenders and simply says “you make a good other” before disappearing. Sora, Donald, and Goofy make their way through the castle, battling the few remaining members of the Organization until they find Kairi, and Xehanort’s Heartless, who is actually Riku. It turns out that in order to help Sora wake up, Riku had to give in to the darkness inside his heart, which changed the way he looked. All of them continue through the castle until they catch up with the King and Diz, who turns out to be the real Ansem. Ansem is trying to use a machine to encode Kingdom Hearts as data, but his machine explodes when the power of Kingdom Hearts proves to be too much. When the explosion clears, Ansem the Wise is gone and Riku has returned to his normal self.
Everyone rushes to the top of the castle to confront Xemnas, the last survivor of the Organization at this point. Xemnas puts up a challenging fight against Sora, but is defeated. With his last bit of strength, Xemnas begs for Kingdom Hearts to give him the power he needs to defeat Sora and his friends. Sora, Donald, and Goofy charge into battle against Xemnas and defeat him, even with the power Kingdom Hearts had given him. When Xemnas disappears, Namine appears and opens a dark portal to get everyone out of the castle before it collapses. The King, Donald, and Goofy go through the portal, but before Kairi, Sora, and Riku go through, Namine rejoins Kairi’s heart and Roxas rejoins Sora’s. Namine is Kairi’s Nobody and Roxas is Sora’s, and unlike all of the other Nobodies, they managed to meet their original selves and be whole again. Kairi goes through the dark portal just in time before it begins to fade, leaving Sora and Riku trapped in the castle.
Xemnas reappears and Sora and Riku team up to fight him for the last time. Their battle brings them to the World of Nothing, and after Xemnas is defeated for good, the two of them are stranded there. A bright light appears and brings them to the Realm of Darkness, where they wait until a message in a bottle washes up on the shore: the message in a bottle that Kairi had let float off into the oceans of the Destiny Islands in search of Sora. As Sora reads the letter, the Door to Light appears and takes them back to the Destiny Islands, where they reunite with all of their friends.
A while later, Sora and Riku are overlooking the ocean and remembering how they had once dreamed of leaving the islands. Kairi comes up to them with a message in a bottle with the King’s seal on it. Sora opens the bottle and reads the message to himself – a message that marks the beginning of a brand new adventure.