Sora

Sora, Donald, and Goofy then resolve to find Riku and the King. While traveling they find a fortress known as Castle Oblivion. Upon entering, they begin to lose their memories and Sora's memories begin to be manipulated by the Organization that is controlling the castle. The Organization use Naminé to make Sora forget Kairi and replace his memories of her with herself. Sora discovers the truth behind the events that have taken place and after defeating the Organization members, he meets with Naminé. She puts Sora, Donald, and Goofy to sleep for one year to restore his memories to their state prior to entering Castle Oblivion.The three awake a year later in Twilight Town and learn about the Nobodies and Organization XIII. Sora also obtains a new ability, "Drive Form", from the fairies Flora, Fauna, and Merryweather, which allows him to transform into more powerful forms and access to new abilities.Sora and the others begin their quest to confront Organization XIII. They eventually find King Mickey and Riku who assist in fighting the organization's leader, Xemnas. Sora and Riku are separated from the others to fight Xemnas one last time. After defeating him they find their way back to Destiny Islands, where they are reunited with Kairi, Donald, Goofy and Mickey.

Riku

After the events in Chain of Memories, Riku confronted Roxas in order to assist DiZ in reuniting him with Sora. During the fight, he used the power of darkness, which converted Riku into the form of Xehanort's Heartless. For most of the story, Riku remains in this form, helping Sora in secret and never showing his face, not wanting Sora or anyone else to discover what had become of him. Riku returns to his original form by the destruction of a machine intended to convert Kingdom Hearts into data. Afterwards, Riku and Sora battle and defeat Xemnas. In the end, they end up on a dark beach, and discuss how strong their friendship is and how much each of them wanted to be like the other, before a portal opens to Destiny Islands. The two use the portal and are sent home.

Kairi

In Kingdom Hearts II, Kairi and all of Sora's friends slowly begin to remember Sora. After Sora's memories had been restored by Naminé, Kairi sends the letter drifting to the sea in hopes of that it will find its way to him. She is later confronted by Axel, who hopes to use Kairi to lure Sora to him. With the help of Pluto, Kairi evades him and heads to Twilight Town, but is captured by Axel soon after. However, Saïx takes Kairi from Axel and imprisons her and Pluto in a jail cell in The World That Never Was. She escapes her cell with the help of Naminé and they are saved from Saïx by Riku, in the guise of Xehanort's Heartless. Riku gives her a Keyblade which she uses to fight off the Heartless that Saïx summons.