Sora and Riku are shown as best friends and rivals as they grew up. They are often seen around the islands battling with wooden swords, racing, and doing anything else that is competitive.
Some time prior to Kingdom Hearts Birth by Sleep, Sora's newly born heart encounters the injured heart of Ventus and mends it, offering to help him restore his broken heart until help is not needed. This allows them to form a connection with one another, and causes Vanitas's face to resemble Sora's.

By the time Sora is four years old, he encounters Terra and Aqua, two Keyblade wielders of the generation before him, on separate occasions. He never spoke with Terra, but they have seen each other on Destiny Islands. Terra shows no interest in Sora because he is unable to sense his potential, and is instead attracted to Riku. Aqua recognizes their friendship as hers to Terra and Ventus and tells Sora to protect Riku if he were to fall into the hands of darkness, which he agrees. Ventus had visited the islands multiple times but had never met Sora face to face.

Near the ending of Kingdom Hearts Birth by Sleep, Sora and Riku rest on a beach. When they prepare to go home, Sora suddenly feels sad and sheds a single tear. Riku tells him that perhaps someone from another world connected to him is sad somewhere and tells him to try to reach him. Sora closes his eyes and reaches out, which results in him being sent to the Awakening and encountering Ventus's lost heart. It had lost its path and must return to slumber, though it is reluctant to do so and asks if it could become a part of Sora's heart. Sora accepts the request saying that as long as he can make it happy by doing so, he is willing to.

One year after the events of Kingdom Hearts Birth by Sleep, a mysterious little girl named Kairi came to their islands from a different place. She was adopted by the mayor, and Sora and Riku quickly became friends with her. Another day, Sora and Riku found a small, hidden cave on their islands. They search the "Secret Place" while discussing Kairi and the meteor shower that had recently fallen. They find a door with no handle at the back of the cave and, because they couldn't open it, they leave, but not before Riku sees the world's Keyhole.

During their childhood, Sora, Riku, and Kairi often wonder about what lay beyond their small world. By the time they reach adolescence, they decide to build a raft, in the hopes of sailing to other worlds. The day when they start construction, Sora dozes off on the shore of the beach and has an odd dream where he travels through an odd, dark realm and battles a massive dark creature. Sora is awakened by Kairi, and he goes to help get the provisions for the raft. However, the night before they set sail, a storm ravages the island along with a strange, dark force. Riku succumbs to the force, claiming he is not afraid of the darkness it so clearly embodied, while Sora tries and fails to save his friend from the darkness.

However, it is during the tempest that Sora first unlocks his potential as a Keyblade wielder, summoning the power of the Kingdom Key to battle the Heartless that now infested his home. He makes his way to the Secret Place where he finds Kairi, who disappears when their bodies meet, forcing Sora to battle the same dark creature from his dream. Sora defeats the monster, but he is swept off the island and thrown into a Corridor of Darkness, which lands him in a world called Traverse Town.

In Traverse Town, Sora meets Donald Duck and Goofy, the respective Royal Court Magician and Captain of the Royal Guard of Disney Castle. Under orders from The King, the pair are searching for two things: a mysterious 'key' and a man called Leon. As the King has disappeared in his own quest, Donald and Goofy accompany Sora and they start searching for their respective friends. In addition to that, Sora finds that his Keyblade might perhaps be the mysterious key the King had asked them to find.

Sora discovers that Riku is also searching for Kairi, though neither of them can find her. Maleficent sees her chance and tells Riku that Sora had replaced him and Kairi for Donald, Goofy, and the Keyblade. With this false knowledge, he sets out to find Kairi on his own as Sora travels to a number of worlds to stop the Heartless. From there, Sora locks the Keyholes out from the reach of the Darkness to protect the worlds' hearts.

His quest allows him to make countless new friends while the power of his heart increases, which also improves his Keyblade's power.

Upon reaching Hollow Bastion, Riku confronts Sora and reveals to him that Riku himself was the true Keyblade master, explaining that Sora "was just the delivery boy". Riku then claims the Keyblade for his own. Despite their guilt at doing so, Donald and Goofy are forced to abandon Sora because of the King's orders: to stay with whoever has the Keyblade. When Beast pulls himself up to continue to the castle, Sora tells him to be careful due to his injuries. However, Beast shrugs off Sora's worries, saying that he would not leave before he completed what he'd come there for; to find Belle. When asked what he came for, Sora realizes that he needs to show the same attitude as the Beast, and continues with him into the entrance hall of the castle.

There Sora meets Riku, Goofy, and Donald once more. Feeling guilty, Donald and Goofy return to Sora's side. Riku then asks Sora, "How do you intend to fight without a weapon?" to which Sora answers, "I don't need the Keyblade. I've got a better weapon. My heart!". Riku taunts Sora, calling his heart pathetic and weak. Sora proceeds to tell him that his friends strengthen his heart. At this, the Keyblade realizes that Riku has turned to darkness, and Sora's heart is far stronger than Riku's, so it returns to Sora. Enraged, Riku fights Sora and loses. Furious at his weakness, he makes the mistake of listening to a mysterious man. Opening his heart fully to darkness, he allows himself to be possessed by this man.

After this, the party encounter Maleficent and defeat her. Using a Keyblade born of six of the Princesses of Hearts' hearts, Riku unlocks the darkness in her heart before stepping away through a Corridor of Darkness. She transforms into a black, fire-breathing dragon from the proliferation of darkness in her heart, but is again defeated and the Heartless swallow her heart. Further into the depths of Hollow Bastion, Sora encounters Riku once more, and he calls himself "Ansem, Seeker of Darkness", who intends to find Kingdom Hearts itself. Although it is difficult fighting his best friend, Sora emerges victorious in the struggle.

Kairi is revealed to be one of the Seven Princesses of Heart who possess the power to open the Final Keyhole that leads to Kingdom Hearts, but because her heart laid within Sora, it cannot open, as explained by "Ansem". In order to return her heart and wake her up, Sora uses the Keyblade of People's Hearts to remove both their hearts, sacrificing his humanity and becoming a Heartless, unknowingly creating Roxas and Naminé, the Nobodies of Sora and Kairi respectively. When he manages to reunite with Kairi after a brief stint as a Heartless, Kairi uses her light to restore his human form.

After regrouping in Traverse Town, Sora decides to return to Hollow Bastion to seal the Final Keyhole while he tries to reclaim Riku from the clutches of "Ansem". Kairi gives Sora her lucky charm (Oathkeeper's keychain) since he insists that she should stay behind, even joking that she would be in his way.

Sora, Donald, and Goofy set sail to Hollow Bastion and seal the Final Keyhole after a battle with a powerful Heartless. The six Princesses of Heart then inform him of a new darkness approaching, and the trio travel to End of the World, the "Heartless world" of all the worlds that fell into darkness, where they confront and defeat "Ansem" once and for all. "Ansem", defeated, calls forth to Kingdom Hearts to fill him with the power of darkness, but Sora proclaims that Kingdom Hearts is not darkness, but light, and "Ansem" is destroyed by the said light.

However, Heartless begin to swarm inside of the door and Sora, Donald, and Goofy rush forward to close it. As they attempt to close the Door to Darkness, Riku and King Mickey appear on the other side of the door and together, King Mickey and Sora seal it from both sides with Sora's Keyblade from the Realm of light and Mickey's Keyblade from the Realm of Darkness. However, Mickey and Riku become trapped behind the door as it closed shut. Riku's last words to Sora before it closed are "Take care of her", referring to Kairi.

As the worlds begin to restore themselves, Sora sees Kairi on a platform of sand that is drifting away. Kairi and Sora are separated from Kairi going back to Destiny Islands. Sora promises to return to her as soon as he finds Riku and King Mickey.

After being separated from his friends, Sora wanders down on a long, meandering path with Donald and Goofy searching for a way to find Riku and Mickey, encountering Pluto on the way. When they reach a crossroad and call it a night, a mysterious man in a long black hooded cloak appears and informs Sora, "Along the road ahead lies something you need. However, in order to claim it, you must lose something that is dear to you". The man disappears and only one path remains. The trio follows the path which leads them to a mysterious castle known as Castle Oblivion. They enter the castle hoping to pick up some clues as to the whereabouts of their friends only to discover, as they ascend the floors of the fortress, they are beginning to lose their memories and become more and more uncertain of what they are truly after. Even Jiminy's journal has been erased of its entries.

Little do they know, their memories are being manipulated by a mysterious organization that seeks to capture and manipulate Sora. To do this, they use Naminé, a young "witch" who could rearrange the chains of memories in a person's mind and create new links between them. In order to make Sora forget Kairi, Naminé begins to replace his memories of Kairi with herself, partly because she is Kairi's Nobody and so is unable to completely erase her from Sora's memories. Meanwhile, a conflict between the members of the Organization leads to several encounters between Sora and Riku, whose memories of Kairi have also been replaced with ones containing Naminé.

The trio's uncertainty builds up to a point where they end up in Twilight Town, a place that Sora is fairly certain that he has never been in, and thus should not exist in his memory. Organization member IV, Vexen, reveals that it is a place that exists on the other side of Sora's heart, but is eliminated by Axel, another member of the Organization, before he can explain anything.

Axel ends up betraying Marluxia, the lord of Castle Oblivion, revealing that Marluxia and Larxene, the newest members of their group, intend to use Sora to overthrow the Organization. Axel manipulates Naminé into doing what she believes is right. Donald and Goofy try to reason with Sora about the whole situation later, but he is so stubborn that he separates from them to go on his own.

On Destiny Islands, Sora is touched to have finally found Naminé, who tries to make him remember who was truly important to him. After taking one look at the lucky charm, it returns to its original form and Naminé takes the temporary form of Kairi. Sora escapes the memory-based Destiny Islands and confronts Naminé, who reveals that she never existed in Sora's memory and that she has been replacing the person most important to him. Riku appears to them again and is again defeated by Sora. When Sora tries to help the injured Riku, he attacks Sora and gains the upper hand. Having left no choice, Naminé uses her power to break Riku's memories, and it causes him to collapse. Larxene comes forth to eliminate Sora and Riku, who is revealed to actually be a Riku Replica, created by Vexen.

When Larxene is about to eliminate Sora, Donald and Goofy catch up to save him. Although Sora had been a jerk to go on his own, they quickly forgive him and state how they would always stay together. Together, they defeat Larxene and Sora forgives a regretful Naminé for her actions. She promises to restore the memories of the trio once they reach the 13th Floor of Castle Oblivion, where Marluxia is waiting for them. Axel attempts to destroy Marluxia himself, but then Marluxia uses Naminé as a human shield. Sora steps in and defeats Axel. After finally catching up to them, Marluxia orders Naminé to completely erase Sora's memory so he could make Sora his puppet; Naminé refuses, but Sora orders her to do so in order to protect her from Marluxia's wrath. Fortunately, the Riku Replica, its true memories returned after his false ones are broken, arrives and saves Naminé before she was able to do so.

Then Sora, Donald, and Goofy step into the thirteenth floor's dimension where they fight Marluxia in an incredible battle.

Once Marluxia was defeated, Naminé asks that they step into Memory Pods that would rearrange their memories back to the way they were at the cost of breaking the links she created. She also informs him that the process will take some time, during which Sora, Donald, and Goofy would sleep as their memories are slowly restored. While they know that they would forget Naminé, Sora promises her that while she was forgotten, she would remain somewhere in his heart, never lost. And when he wakes up, they would become friends for real.

Right before he went to sleep, Naminé informs him that some of his memories are unreachable and asks him to remember Kairi, because his memory of her is the light that would bring them all back. Sora then uses most of the power of his memories to remember Kairi before going to sleep for real.

One year later, Sora, Donald, and Goofy awake in the basement of the Old Mansion located in Twilight Town with their former memories restored, although they cannot remember what happened in Castle Oblivion. But before they awake in Twilight Town, Roxas comes to see Sora and eventually fuses with him. Continuing their journey to find Riku and King Mickey, they set out traveling across new worlds, meeting old friends and enemies from the original Kingdom Hearts game while also making new friends. They continue the battle against the Heartless and now a new threat, the remaining members of the Organization they encountered in Chain of Memories.

Soon after exploring Twilight Town, Sora and company head off to the Mysterious Tower and Sora obtains new attire—on the advice of master sorcerer Yen Sid considering Sora's first game outfit to be "too small"—from Flora, Fauna, and Merryweather. The new outfit enables Sora to transform into his Drive Form and attain special powers for each of them. The source of the clothing's magic is linked to Sora's heart, which is connected to everyone Sora had befriended including Donald and Goofy. Sora was referred to as the "Key that connects everything" by Yen Sid which is how Naminé's memory manipulation works.

Sora expresses his determination to bring Riku back home with him to Destiny Islands, where Kairi is waiting for them. The quest gets more complicated when Kairi herself gets kidnapped by Axel. Pete (who works for the resurrected Maleficent) and Organization XIII are causing trouble in the other worlds, and King Mickey refuses to give information regarding Riku. Sora must also discover why some of the members of Organization XIII address him as Roxas even after he clearly states his name is Sora. He travels to other worlds to find Riku and the King, help the worlds and stop Organization XIII. His new journey brings him to meet up with some old friends and make new ones.

At one point in the storyline, Donald and Goofy's homeworld becomes infested with Heartless, which is rather unusual considering their world's protection, and Sora visits their castle for the first time. While Donald and Goofy set out to warn the castle's residents about the danger, Sora escorts Queen Minnie to the audience chamber where the Cornerstone of Light is hidden under. He finds out that Pete and Maleficent have found a doorway to Timeless River, a past timeline of their world before the castle was built. With some help from Merlin, Sora, Donald, and Goofy travel through time and manage to stop Pete from destroying the Cornerstone of Light in the past, which also saves the castle for good.

Sora, with the help of the Hayner, Pence, Olette (three friends of Roxas in DiZ's simulated Twilight Town), and Axel (who sacrifices his existence), manages to find the route to the World That Never Was: which is the stronghold of the Organization, where Kingdom Hearts, created by gathering the countless hearts from the Heartless slain by Sora's Keyblade, resides. Soon after entering the world however, in the area of Memory's Skyscraper, Sora's group is ambushed by Samurai Nobodies and Sora is forced into a showdown with an Organization member, who turns out to be Roxas (disguised in his former Organization XIII cloak) on a platform of Awakening.

At the start of the fight, Sora asks who Roxas is, and he answers "Someone from the dark.", then asks Sora: "Tell me...Tell me why he picked you!".

As Roxas is above and Sora below, he sees the picture of Riku, Kairi, Donald, and Goofy (as the platform's design). Roxas then says, "I see, that's why.", and continues the fight. Roxas knocks the Keyblade out of Sora's grasp, and as he goes to retrieve it, Roxas pins it down with his own Keyblade. Sora then reaches out for his Keyblade, which disappears and reappears in his hands, after which Sora quickly strikes while Roxas stands shocked, not knowing how that happened.

Ultimately, Sora's control over his Keyblade gave him the edge over Roxas, who collapses and reveals his face. As he and the scenery disappear, Roxas says to Sora "You make a good other." Sora reappears next to Donald and Goofy, who tell him that while he disappeared, they had to fight some Nobodies, and they continue towards the massive castle where Kairi awaits them.

Afterwards, Sora, Donald, Goofy, and King Mickey storm the Castle in search of their friends. They meet Saïx at the Hall of Empty Melodies, who tells that Kingdom Hearts is near completion, and it only needed "one more dose from the Keyblade Bearer." He summons hordes of Shadows and disappears to go after Maleficent and Pete who were also in the castle. The Heartless overpower Sora, but are destroyed by a rain of laser bullets. Sora then engages in a battle with Xigbar and soon defeats him. He finds Kairi and Riku (with the appearance of Ansem, Seeker of Darkness, which is the price he paid to help Sora wake up).

Sora, Riku, Kairi, Donald, and Goofy make it to the Proof of Existence of the Organization, in which there are only two places to go. They enter one of the odd pathways only to encounter Luxord. Although Luxord traps everyone but Sora in cards, he is still defeated by the Keyblade master. Next, they enter Addled Impasse where they find Saïx staring up at the moon. Saïx points out that only Roxas could have made it this far in one piece and Sora gets angry and prepares to attack him. Saïx blows Riku and Kairi away and uses the power of the moon to fight. After one of Sora's most difficult battles, Saïx is finally defeated. Sora then questions who Roxas is and why he was constantly being called by that name when Riku finally reveals to Sora that Roxas is his Nobody.

With the mysteries of Roxas's identity finally solved, they continue on. Fighting their way up the winding paths of the Castle That Never Was, Sora, Riku, and the others encounter King Mickey and DiZ, now revealed to be the former ruler of Radiant Garden, before it was taken over and renamed Hollow Bastion, Ansem the Wise, who was trying to absorb Kingdom Hearts into his machine and encode it as data. Xemnas appears to see who is tampering with Kingdom Hearts and finds his old teacher. Then Xemnas finally tells Sora and the others of his true plan, to make a Kingdom out of hearts. One that he would rule. Unfortunately, Kingdom Hearts proved too strong for Ansem's machine, and with his final words, he tells Sora the rest is up to him and tells Roxas, "Roxas, I doubt you can hear me but, I am sorry", before the machine explodes, taking Ansem with it. The energy released in the explosion destroys a good deal of Kingdom Hearts and reverts Riku's appearance to the way it was.

Near the pinnacle of the castle, Heartless appear in vast hordes. Maleficent and Pete show up and stall them while the party heads toward their final battle. When they reach the Altar of Naught at the pinnacle of the castle, they confront Xemnas, the leader of Organization XIII. After a short conversation with the Nobody, Sora is taken by Xemnas to the front of Memory's Skyscraper for a one-on-one battle. After an intense fight, Sora defeats Xemnas and is transported back to his friends.

However, Xemnas appears again and, despite the protests of the group, enters and absorbs Kingdom Hearts. The party was in luck though, and by the will of the worlds a door to Kingdom Hearts is made. Sora, Riku and the King open the door with their Keyblades, breaking the barrier separating them from Xemnas. The party enters but Sora, Riku, Donald and Goofy become separated from King Mickey and Kairi because of Xemnas.

Inside, they discover that Kingdom Hearts was made by the Superior to look like the World That Never Was. They charge through and quickly get to Xemnas and battle him, with Xemnas in armor using the tactics of the rest of the Organization. After they seemingly defeat the Organization leader and return to the Altar of Naught, Roxas emerges from Sora's body to speak with Naminé before she fuses with Kairi. Before this, Naminé opens a door to lead them out of the World That Never Was. He informs Sora that whenever he and Kairi are together, Roxas and Naminé will be together as well. Naminé then joins with Kairi to complete herself, while Roxas returns to Sora's body making Sora whole.

Unfortunately, before Sora and Riku can enter the Corridor, Xemnas attacks once again on the Captain's Seat of an enormous Dragon Nobody. In an epic air battle they manage to defeat this form of Xemnas as well. Riku is injured by Xemnas, who strikes at both with his Ethereal Blades. Falling through the air on the brink of defeat, Sora grabs Riku's Keyblade and batters Xemnas with both. Returning it to Riku, they use a bolt of light and dark energy to finish off Xemnas.

Afterward, Sora must help Riku walk, as he sustained a heavy injury from one of Xemnas's Ethereal Blades. They wander through the eternal abyss and eventually come to a dark beach under a pale moon, the Dark Margin. Resting at the shoreline, they discuss their adventures and friendship, and come to the conclusion that they did what they set out to do, and agreed that "If worlds are made of light and darkness, we'll be the darkness." The Realm of Light was safe, and they could now sit and let peace envelop them.

As they listen to the waves, a bottle containing a letter that Kairi wrote washes onto the shore. Riku picks it up, and, after reading it, gives it to Sora, believing him to be the proper recipient. The letter reads:

"Thinking of you, wherever you are.
We pray for our sorrows to end, and hope that our hearts will blend.
Now I will step forward to realize this wish.
And who knows:
starting a new journey may not be so hard,
or maybe it has already begun.
There are many worlds, but they share the same sky —
one sky, one destiny."
-Kairi

After Sora reads it, the door to light appears, and both Sora and Riku use it to return to their homeworld: Destiny Islands.

Having brought Riku back home and reunited at last with all his friends in one piece, Sora is finally able to return Kairi's lucky charm to her, saying "We-We're back!" and Kairi corrects him saying "You're home". Kairi extends her arm to Sora, and he grasps her hand while simultaneously returning the charm he kept for her all this time.

Some time later, Sora is walking around in the Secret Cave. He smiles while looking at all the pictures he and Kairi had drawn over the years. He glances down at the picture of Kairi and himself. He sees that Kairi drew the other half of a paopu fruit, and smiles to himself, mimicking Kairi's actions from a year ago.

Much later, Sora asks Riku what he thinks the door to light was. Riku replies that it was Sora's heart; "It's always closer than you think". Kairi runs up to them breathlessly and gives them a bottle she found, containing a letter from King Mickey. The trio reads the letter.

In Ansem and Aqua's encounter deep within the realm of darkness, it is revealed by Ansem that he has hidden his research (most likely the one concerning Kingdom Hearts and the realms of Light and Darkness) inside of Sora, during his sleep in-between Kingdom Hearts: Chain of Memories and Kingdom Hearts II. He then proceeds to say that he would like to believe that "this boy" will be the one who will open the "right door" and save all of those whose lives were ruined by his research, including himself and Aqua.

Later, after Sora has received Mickey's newest letter, he sits on the paopu tree while holding the message from King Mickey, staring off into the sunset.

It is revealed that he has now read the contents of the message and must venture out on a new quest to find Terra, Aqua, and Ventus, as well as the others connected to him, and save them from their suffering. As he says goodbye to Kairi, she gives Sora her Wayfinder again, telling him, "See you soon".

Sora and Riku are first seen at Destiny Islands in their Kingdom Hearts outfits, having been sent back by Yen Sid to the time shortly before their world falls to sleep. Sora wonders how far the raft can take them. They soon begin to sail on the ocean, but they end up in a storm and undergo an attack by Ursula, whom Sora recognizes. After the battle, they end up in a whirlpool and get separated. A keyhole opens, allowing Sora and Riku entrance to the Sleeping Worlds.

After this, a conversation between the kids and Yen Sid is shown. Yen Sid tells them about Master Xehanort and that both of them should become Keyblade Masters in order to face this new threat. Sora claims that even without taking the Mark of Mastery exam, no one can beat the two of them. Yen Sid then sends them to the Realm of Sleep.

Sora wakes up in Traverse Town, noticing the change of his outfit, which he presumes is "more of Master Yen Sid's magic". He immediately goes searching for Riku, though he runs into Neku Sakuraba instead. Neku explains the concept of Dream Eaters to Sora and leads him to the Third District, where a hooded figure attacks them. Sora attempts to help Neku but eventually falls asleep.

Sora later wakes up and chooses to find Neku, discovering new areas of Traverse Town that he's never seen before. He meets Rhyme, who helps on his search for Neku; when they find him, Neku apologizes to Sora. Rhyme suddenly disappears and more hooded figures appear, only to summon a giant Dream Eater, which Sora defeats. Sora then sees a transparent Riku, who disappears into Young Xehanort. Joshua then appears with Rhyme and Neku, and Sora realizes that he and Riku are parallel to each other.

Sora travels to La Cité des Cloches, where Judge Claude Frollo stops him. He wonders if Sora is a gypsy, because of his unusual clothes and appearance. When Phoebus comes to tell that there are monsters on the loose, Sora runs to fight them and eventually meets Quasimodo, who saves Esmeralda. Sora and Phoebus follow them to Notre Dame's attics. After some time, Sora meets Phoebus and Quasimodo again and they travel to the Court of Miracles, where Sora gets knocked out by a Dream Eater, while Frollo takes Esmeralda away. Sora wakes up and travels back to the city, where Quasimodo saves Esmeralda. Sora destroys a Dream Eater and sees how Frollo falls to his defeat, while Phoebus saves Quasimodo from the same fate. In the cathedral, Sora says farewell to Quasimodo and the others. When he is about to leave, Young Xehanort appears and calls him a hypocrite for freeing one prisoner but keeping another. Vanitas's image also appears besides Young Xehanort, making Sora confused as the villain vanishes to darkness and Keyhole of Sleep appears. Sora unlocks it and wonders what Xehanort meant by saying his heart is a prison.

Sora then travels to The Grid, where he meets guards. When introducing himself, guards try to take him prisoner, but Sora escapes. He meets Rinzler first, then is introduced as well to Kevin, Sam, and Quorra, who inform him that Rinzler is actually Tron. Believing that Tron remembers him, Sora is determined to meet him. With Quorra's help, Sora finds Rinzler and tells him to try and remember him; however, Rinzler attacks him and Quorra before fleeing. Young Xehanort then reappears, this time with Xemnas. Xemnas tells that Sora he has so many memories that can't be his alone. Sora is then sent away by strong wind, while Xemnas and Xehanort disappear. When meeting again with Rinzler and CLU, CLU tells Sora that he will turn Rinzler back to Tron, if Sora hands over his Keyblade. Sora tells that he will not give it up since it gives him the "chance to make everyone happy". CLU then sends Rinzler to attack Sora. After a battle, Sora tries to remind Tron again, but CLU throws his identity disc at Sora, causing Rinzler to push Sora to safety before falling out of sight. CLU leaves to retrieve Rinzler, and Sora unlocks The Grid's Keyhole of Sleep.

When Sora arrives at The World That Never Was, where he lands near Memory's Skyscraper and encounters Xigbar. Xigbar explains that Ansem, the brown-robed man, had contact with Sora when he first entered the Sleeping Worlds from Destiny Islands, allowing the Organization to track Sora through his dreams and lead him to this world. Angered, Sora blames Xigbar for what happened and prepares to fight, and Xigbar notes that he is glaring at him like Ventus always did, even calling Sora as "Roxas". He then jumps above Sora and fires twelve arrows around him, eleven of which spawn unknown hooded figures, and the remaining one spawning Young Xehanort, who offers his hand and tells Sora to come with him. Sora then immediately drops.

Sora wakes, realizing he is at Destiny Islands, where Young Xehanort is sitting just next to him. They watch the other Young Xehanort, who meets "Ansem", who grants him abilities to time travel. "Ansem" then approaches Sora, who shouts in fear. In the next scene, Sora and Young Xehanort are still on the islands during nighttime. They see Sora running into the secret cave and they talk a little until Kairi steps out from the cave towards Sora. The next scene shows Sora falling from the air with other Soras. The real Sora lands on his feet and sees the Sora copies moving about Traverse Town. Young Xehanort talks to him about his journeys through Traverse Town.

Sora then wakes up at Dark City back in his Kingdom Hearts II attire. He immediately sees Naminé, who tries to run away from him, but Sora grabs her arm. Namine then turns into Xion. Sora is unaware of her identity, yet unconsciously sheds a tear as she runs off. Sora runs after her, only to meet Roxas. Roxas tells Sora that they should share all memories and emotions, but Sora denies this by saying that Roxas is just Roxas and they are not the same. He also thinks that Roxas should be able to exist by himself. Roxas is surprised, and shares his painful memories with Sora before vanishing. Sora starts to blame Organization XIII for what they have done, but then he hears Riku's voice that warns him about chasing after illusions.

Sora later meets Kairi and Riku who turn into Aqua and Terra. Sora then turns into Ventus and stares at them. Aqua and Terra turn around and walk away and Ventus is trying to reach them, but he slows down and turns back into Sora. Sora then watches as Riku and Kairi vanish, changing into Terra and Aqua for a second. He then remembers his meeting with Aqua, a long time ago.

Sora meets Xigbar and Xemnas again and they have a conversation, where Xemnas reveals that Organization XIII was created in order to form the Thirteen Hearts of Darkness, which Master Xehanort could use in the future. Kingdom Hearts was created in order to move pieces of Xehanort's heart into thirteen vessels. However, Xemnas discovered that Nobodies actually can cultivate new hearts, so he and Xigbar left the others in the dark about this fact to maintain their loyalty to their cause. Xigbar then reveals to Sora that he is chosen to be the final vessel of Xehanort's heart, after which Sora summons his Keyblade, saying "Connected hearts are my power." Then Kairi, Riku, Roxas, Xion, Ventus, Aqua, Terra, Mickey, Donald, and Goofy appear behind him as illusions, stunning Xigbar, who tells Xemnas to take care of Sora. After a fight, Sora is completely tired and lies on the ground with darkness surrounding his body. Young Xehanort then appears, telling him that his clothes, bearing a sneaky Recusant's Sigil, feed the darkness within him, since, unlike Riku, Sora never made any protection against his inner darkness.

Sora is then seen sitting at Where Nothing Gathers. Riku and Mickey are attempting to save him when Master Xehanort attempts to split Sora's heart and make him one of his incarnations. Though Xemnas and Ansem subdue them, Lea appears and blocks Master Xehanort's attack. After that, Master Xehanort, along with his new Organization XIII, vanishes. Riku, Lea, and the others return to the Mysterious Tower, where Yen Sid sends Riku into Sora's heart in order to save him from falling into darkness. Whilst there, Riku discovers that Roxas, Ventus, and Xion still reside within Sora's heart, as does a copy of Ansem the Wise.

After that, Sora wakes up and he, Donald, and Goofy have a tea party; Riku wakes up and Sora hugs him, relieved his friend is okay as well. Yen Sid then tells them that only Riku passed the Mark of Mastery. Sora, however, does not appear to be sad at all, and he even congratulates Riku. Lea then reveals that he also has a Keyblade and that he will help them in the near future. Sora then returns to the Realm of Sleep in order to thank all the Spirit Dream Eaters he had become friends with.

Sometime later, Sora returns to the Mysterious Tower from a secret mission and is dismayed to learn that Riku, Mickey, and Lea have left for their own missions. Yen Sid then tells Sora that he has, once again, lost most of his power after being captured by Master Xehanort. He then goes on to tell him that he must reclaim his lost power by following his heart, and reuniting with his friends, and advises Sora to visit a hero who had lost and then regained his strength.

Sora, Donald, and Goofy depart, but don't get very far because Sora doesn't know where to go. He and Donald begin arguing about this, until Goofy says, "May your heart be your guiding key," an old saying of the ancient Keyblade wielders. Sora repeats it to himself and realizes where they must go. He opens a gateway to Olympus Coliseum, which they then go through to visit Hercules.

Following Master Xehanort's return, Yen Sid begins preparing for seven Keyblade wielders to counteract Xehanort's plan to forge the χ-blade using a reconstituted Organization XIII. Sora, who was nearly taken over by Xehanort, (As depicted in the 2012 game Kingdom Hearts 3D: Dream Drop Distance.) discovers that he has lost much of his own strength as a result. Accompanied by Donald Duck and Goofy, Sora resumes his travels across other worlds to regain his "power of waking", the ability to restore lost hearts. Meanwhile, Riku and King Mickey search the realm of darkness for Aqua, while Kairi and Lea train to properly wield their newly obtained Keyblades.

Continuing from Kingdom Hearts 0.2 Birth by Sleep -A fragmentary passage-, Sora decides to embark on a journey to restore his powers along with Donald and Goofy. Sora first visits the Mysterious Tower after receiving a request from Yen Sid to go on a secret mission. Yen Sid tells him, Donald, and Goofy that he needs to visit Hercules in order to restore his lost powers. Upon entering the Gummi Ship, Sora appears to have forgotten how to activate it. Although he and Donald bicker, Goofy reminds him that "may your heart be your guiding key." Realizing the meaning behind this message, Sora understands his purpose and opens a portal to Olympus using his Keyblade. The trio proceeds to enter the gate with a newfound demeanor.

Upon arriving in Olympus, Sora questions why the ship didn't directly land near the Coliseum, in which Donald tells him that he was the one who opened the gate. Regardless, Sora vows to reach his destination by climbing up the mountains. During their climb, the trio encounters Hades, who uses the Titans' powers to knock them off the mountains. As Sora, Donald, and Goofy are sent flying, Hercules spots them and saves them from crash landing into Olympus (though Donald lands near a golden statue).

During their travels, Sora and Riku are contacted by Ienzo, who discovers via Ansem the Wise's research data that Sora's body contains the hearts of Roxas, Ventus, and Xion. Riku surmises that the Organization's members from the past are using artificial human replicas created by Vexen as vessels that enable their existence in the present, which inspires Sora to restore Roxas by transferring his heart into a replica body. Meanwhile, the Heartless Ansem enters the realm of darkness and kidnaps Ansem the Wise, corrupting Aqua's heart in the process. However, Vexen reveals himself to be a double agent loyal to Ansem the Wise, whom he helps rescue before sending a spare replica to Ienzo for Roxas to inhabit.

Riku and Mickey eventually locate and battle the corrupted Aqua in the realm of darkness. At the same time, Sora discovers Master Eraqus's Keyblade on the Destiny Islands and uses it to enter the dark realm, where he exorcises the darkness from Aqua and returns her to the realm of light. Sora, Donald, and Goofy then follow Aqua to Castle Oblivion, which she transforms back into the Land of Departure to awaken Ventus. When she is attacked by Vanitas, Sora rediscovers his power of waking and revives Ventus, who fends Vanitas off.

The seven Keyblade wielders depart for the Keyblade Graveyard to battle the Organization, only to be quickly consumed by a swarm of Heartless summoned by the possessed Terra. Awakening in a limbo realm called the Final World, Sora is guided back to the realm of light by Kairi and uses the power of waking to revive his friends. Returning moments before their initial defeat, the guardians of light successfully destroy most of the Organization's members; in the process, Terra regains control of his body and reunites with Aqua and Ventus, while Lea reunites with Xion, whom Vexen recreated for the Organization, and Roxas, who regains his own heart to protect Lea and Xion.

Once Xehanort remains the last Organization member, he provokes Sora into attacking him by destroying Kairi's body, allowing Xehanort to acquire the χ-blade and summon Kingdom Hearts. Using Xehanort's power of time travel against him, Sora, Donald, and Goofy transport him to his boyhood training grounds of Scala ad Caelum, where they defeat him. After the other Keyblade wielders rejoin them, Eraqus's heart emerges from Terra and convinces Xehanort to surrender. Xehanort dies shortly after, his heart ascending to Kingdom Hearts with Eraqus, while Sora and his friends use the χ-blade to close it and return to the Keyblade Graveyard. Sora decides to use the power of waking to revive Kairi; despite warnings that his repeated misuse of this power could result in him losing his heart, Sora promises to return. Afterwards, Sora's friends gather at the Destiny Islands for a celebration, where Kairi stays beside Sora before he fades away.