Sora always had some sort of mental illness and took the raft out to test it during a storm but fell off and banged his head, ending up in a hospital with a coma. The following happened:
* Kingdom Hearts - The destruction of Destiny Islands symbolises the disappearance of Sora's life hence why his friends disappear. Due to Sora's uncontrolled jealousy towards Riku, Sora manifests it as Riku turning evil. Kairi disappears symbolising Sora's despair at now being with her. Donald and Goofy are created to replace them and keep him company until he reunites with his friends. Xehanort, Maleficent and the Heartless symbolise Sora's illness and pain which threatens to devour his mind/the worlds. Kingdom Hearts symbolises Sora's brain, and its destruction will lead to Sora's permanent hospitalisation/death.
* Chain of Memories - The events of this chapter are caused by a doctor trying a new medicine on Sora. It causes a reaction, causing Sora to suffer from a relapse and fall further into his coma. The medicine's effects appear as Namine, altering Sora's mind and damaging his memories of his life and Kairi. Sora grows hateful towards the doctors and hospital, creating the present Organization XIII members and Castle Oblivion. The doctors manage to neutralise the medicine's effects, causing Sora to go into his year-long sleep. Riku's storyline symbolises Sora dealing with his jealousy towards his friend.
* 358/2 Days - Sora's reaction to the medicine warps his mind, causing him to create Roxas and Xion as alternate personalities. Riku and a doctor who becomes the basis of Axel's change of heart talk to him, causing Xion to experience her body changes and eventually turn into Sora. A psychiatrist is brought in to deal with Sora's personalities, becoming DiZ in his mind. Xion is eventually removed, much to Sora's anguish. Roxas then is subdued by the psychiatrist, symbolised by his capture by Riku and imprisoned in the fake Twilight Town.
* Kingdom Hearts II - Riku, the doctor and psychiatrist speak to Roxas one final time and manage to bring Sora's personality back to the surface. However, lingering effects of his illness resurface, recreating Maleficent and introducing the remaining Organization members who seek to destroy his mind again. Riku is still absent, symbolising Sora's shame for envying his best friend although the real Riku guides him by talking to him. Kairi's kidnapping is caused by an incident where Kairi and the doctor argue in front of Sora, Axel becoming the perpetrator. King Mickey plays a larger role, established long ago as a parental figure of sorts. After Axel's death (the doctor's departure), Sora deals with Roxas' invading personality and makes peace with it so to speak, before overcoming his illness once again with the Organization's defeat. Ansem the Wise's "death" is caused by the psychiatrist's departure. Sora speaks with Riku and apologises, the conversation between heard by Sora and created in the world of darkness. Sora and Riku return to Destiny Islands, bringing Sora into a better condition which now only requires him to awaken himself.
* Birth By Sleep - Since this is a prequel, most events were made up by Sora's psyche. Sora is moved to another ward by the hospital administrator (Master Xehanort), Sora believing he wishes him to have another relapse. His own fears take the form of Vanitas. Sora creates new characters in the form of Terra, Aqua and Ventus, based on his parents and a renewed version of Roxas' personality. Master Eraqus is based on his new doctor. Sora's growing fears and paranoia, along with his desire to wake up, lead to each of the heroes' tragic endings (Eraqus' death, Ven's coma to symbolise his own, Aqua's sacrifices and Terra's imprisonment). However, Sora overcomes his anguish and gives the inner Xehanort amnesia as a result. The letter Mickey sends to Sora is the final catalyst Sora uses to decide to deal with all his inner personalities before choosing to awake.
Character Interpretations
Sora - In a coma. His inner self represents what he wants to be - a courageous warrior who fights evil. The events which happen to him and his friends are caused by events in hospital.Riku - Sora's best friend. Sora's own jealousy towards Riku and how he deals with it causes the character to turn evil and go through an anti-hero period.
Kairi - Sora's love interest. Her disappearance and coma-like state is based on Sora's desire to be in her company. She is forgotten by Sora when the Namine medicine damages his memories, and waits on Destiny Islands until Sora can properly remember her and is brought into the main adventures as a result of him remembering her.
Donald and Goofy - Created to replace Riku and Kairi as close friends, based on aspects of Sora's personality.
King Mickey - Created as a parental figure.
Xehanort/Maleficent/Pete/Organization XIII/Nobodies - Symbolises the illness and brain damage Sora suffers from. The Castle Oblivion Organization members also symbolise Sora's hatred for the hospital and doctors.
Namine - Symbolises the poor medicine which has damaged Sora's mind. Appears as a victim due to Sora's belief the doctors are against him.
DiZ - Symbolises the psychiatrist who helps Sora regain control of his mind.
Roxas and Xion - Alternate personalities created by Sora after the effects of the Namine medicine. They are slowly repressed by Riku and the psychiatrist (DiZ). Xion is removed completely whilst Roxas is convinced to allow Sora to resurface.
Axel - Based on a doctor who Sora bonds with. The doctor forms bonds with Roxas and Xion's personalities and helps coax Sora back into control.
Terra - Based on Sora's dad.
Aqua - Based on Sora's mum.
Ventus - A new interpretation of Roxas.
Vanitas - Symbolises Sora's fears.
Master Xehanort - Based on the hospital administrator who moved Sora to another ward, and a new incarnation of Sora's illness.
Master Eraqus - Based on a doctor who replaced Axel's inspiration.
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KH Theory
FanfictionThis is a theory I found on deviantart that says that KH series took place inside Sora's head. I copied it directly, but I don't know the author.