Kingdom Hearts begins on Destiny Islands, where Sora, Riku, and Kairi live. The three friends want to leave the islands to explore new worlds and have prepared a raft for this purpose.One night, the islands are attacked by darkness and shadow creatures—the Heartless. Sora seeks out his friends, finding Riku, who disappears into darkness. At the same time, Sora obtains the Keyblade. The islands are presumed as destroyed, and Sora is left adrift. Meanwhile, King Mickey has left his world to deal with the increasing darkness and left instructions for mage Donald and knight Goofy to find the "key" that will save the King and the Worlds.

Donald and Goofy use the Gummi Ship to travel to Traverse Town, where Sora has drifted. Sora encounters the Heartless again, and meets Leon, who explains the Heartless are beings that consume hearts, and that the Keyblade is the only weapon capable of defeating them^. A man named Ansem is said to have studied the Heartless. Sora meets Donald and Goofy and the three decide to travel together; Donald and Goofy to find Mickey, and Sora to find Kairi and Riku. The three go to various worlds based on Disney films, finding that the Keyblade also locks "Keyholes", passages the Heartless use to take the heart of a world. A group of Disney villains, led by Maleficent, seek out the seven Princesses of Heart to unlock the Keyhole that leads to Kingdom Hearts, a repository of knowledge and power and the source of all hearts. This group includes Riku, whom Maleficent promises she will help in finding Kairi. Maleficent sows distrust in Riku, telling him Sora has abandoned him and Kairi for new friends and the Keyblade. An increasingly antagonistic Riku finds Kairi's body, but cannot find her heart.

Sora and his friends eventually arrive at Hollow Bastion, the homeworld of Ansem and the headquarters of Maleficent. Riku takes the Keyblade from Sora, revealing him as the true Keyblade master and that Sora only received it in his absence.Donald and Goofy, taking their order to follow the "key" seriously, leave with Riku. Sora challenges Riku, stating his heart derives strength from his friends; his friends return to him, as does the Keyblade. In his shame, Riku meets a cloaked man who goads him to give into the darkness. The three engage and kill Maleficent, but then meet a strangely-behaved Riku with a Keyblade that unlocks hearts. Sora finds Kairi's body and Riku, who reveals himself to be Ansem, possessing Riku's body^. Ansem explains that Kairi is a Princess of Heart and her heart was trapped within Sora's body since Destiny Islands were destroyed. After defeating Ansem, Sora uses Ansem's Keyblade to unlock his heart by impaling himself, releasing both his and Kairi's heart. Kairi's heart returns to her body, in turn completing the final Keyhole, while Sora becomes a Heartless. Sora is restored to human form by Kairi and resolves to confront Ansem.

Ansem is found in End of the World, the combined remnants of worlds taken by the Heartless Ansem explains his belief that the nature of the heart revolves around darkness, and he seeks Kingdom Hearts, as that would be the ultimate darkness. However, upon opening the door to Kingdom Hearts, it reveals its light, overwhelming and destroying Ansem. Beyond the door are King Mickey and Riku, and they help Sora and the others close the door, as there are many Heartless beyond it. Mickey and Sora use their Keyblades to lock the door. The worlds lost to the Heartless reconstruct themselves, separating Sora and Kairi. The game concludes as Sora, Donald, and Goofy resolve to find Riku and Mickey^.

Final Fantasy X-2 begins as Yuna, Rikku and Paine recover Yuna's stolen Garment Sphere from the Leblanc Syndicate in the first of several encounters in which they vie for spheres. The game is punctuated by a narration of Yuna addressing Tidus, as though she is recounting the events of the game to him as they occur in a style reminiscent of Tidus' own narration in Final Fantasy X. Although Yuna's quest is to find clues that may lead her to Tidus, much of the storyline of the game follows the clash of the factions that have established themselves in the time since the coming of the Eternal Calm in Final Fantasy X, and the uncovering of hidden legacies from Spira's ancient history. A significant portion of the game's events are unnecessary for the completion of the main storyline, but much of the depth of the story—including characterization and background details—are featured in the optional content, which generally follows how each part of Spira is healing in the time since the passing of Sin.

As the game progresses, the hostilities between the Youth League and New Yevon build to a head. In the meantime, the Gullwings discover an ancient sphere containing images of an enormous machina weapon called "Vegnagun" that was secretly buried beneath the city of Bevelle. The weapon has enough power to threaten all of Spira, and, moreover, it is revealed to the player that Vegnagun is unable to distinguish friend from foe once activated.The Gullwings then join forces with the Leblanc Syndicate to investigate the underground areas of the city in an attempt to destroy the machine before it can be used by either side in the upcoming conflict. However, discovering a large tunnel recently dug into the floor of the weapon's chamber, they realize that Vegnagun has apparently been moved to the Farplane, located at Spira's core.

Disagreements between Spira's factions are soon punctuated further after the disappearance of Baralai, Nooj and Gippal—the leaders of New Yevon, the Youth League and the Machine Faction respectively. Returning to the underground areas of Bevelle, the Gullwings discover the missing faction leaders discussing Vegnagun and learn that the machine's artificial intelligence allows it to detect hostility and to respond by activating itself and fleeing.Additionally, it is revealed that Nooj had come to Bevelle with the intention of destroying Vegnagun previously, prompting it to flee to the Farplane. The player then learns that Paine had once been friends with all three men, assigned to be their sphere recorder while they were candidates for the Crimson Squad, an elite group intended to be assigned leadership of Crusader chapters across Spira.

Two years earlier in a cave beneath Mushroom Rock Road called "the Den of Woe", just before the failed Operation Mi'ihen, the squad's final exercise was conducted. Within the cave, the various squad candidates were swarmed by pyreflies and driven to kill one another. The only survivors were Paine, Baralai, Gippal and Nooj, who were themselves targeted by the Yevon order afterward when they revealed having seen images of Vegnagun while in the cave. Soon after, Nooj shot his surviving comrades and left them to die, severing the friendship the group had with one another. However, at this time, it is revealed that he was not acting of his own accord when he shot them. The feelings that drove the squad members to kill one another are revealed to have been the despair of the game's antagonist, Shuyin, who died 1000 years earlier. Before the four survivors could leave the cave, the spirit of Shuyin—requiring a host in order to interact with the world physically had possessed Nooj, and later forced him to shoot his comrades. In the time since, Shuyin had been subtly goading Nooj on a subconscious level, coercing him to approach Vegnagun so that he could use Nooj's body to control it.

The player learns that 1000 years before the game, Shuyin was a famous blitzball player in the high-tech metropolis of Zanarkand, and the lover of a popular songstress and summoner—Lenne. Shuyin's memory would then form Tidus in Dream Zanarkand in the events of Final Fantasy X. The two lived during Zanarkand's war with the more powerful Bevelle, and during the course of the war, Zanarkand ordered all summoners to the front lines, separating the couple. Believing that Lenne would die in battle, Shuyin decided that the only way to save her was to infiltrate Bevelle, commandeer Vegnagun, and use it to destroy Zanarkand's enemies. However, Lenne perceived Shuyin's intentions, and—unwilling to allow him to take the lives of many others for her sake—followed him. When she caught up to Shuyin in Bevelle, he had only just begun to operate Vegnagun's control panel, an organ integrated into its head. Before he could use the giant cannon located in its mouth to destroy the city, Lenne asked him to stop. Shuyin did as she asked, but a group of Bevelle soldiers arrived a moment later and shot the couple. Fatally injured, Shuyin failed to hear Lenne saying that she loved him before they died.

Over the course of the following 1000 years, Shuyin's despair and resentment over his failure to save Lenne bonded to pyreflies and caused him to constantly experience the anguish of that moment.Over time, his despair became so powerful that it began acting on its own,and he came to believe that—in addition to helping the world—he would fade away with Lenne if he destroyed Spira.

Now with an understanding of Shuyin's hatred for war, Yuna manages to return to the surface and the Gullwings organize a concert to which everyone in Spira is invited, supporters of the Youth League and New Yevon alike. Additionally, the Songstress dressphere worn by Yuna is revealed to be comprised of Lenne's memories, resulting in a sphere screen projecting them to everyone in attendance during the concert. Witnessing images of Shuyin and Lenne's last moments, Spira's citizens begin to understand the unproductive nature of their disagreements. The player then learns that it was because of Lenne's memories that Shuyin had mistaken Yuna for Lenne and she had felt affection toward him.

Although the factional fighting has ceased, Shuyin has nearly carried out his plan to use Vegnagun's cannon to destroy the planet from beneath its surface. Joining forces with the Leblanc Syndicate once again, the Gullwings make their way to the Farplane and find Gippal and Nooj already battling Vegnagun. Working together, they manage to disable the giant machina before its cannon can fire at Spira. Finally confronting Shuyin, Lenne's consciousness emerges from the Songstress dressphere and convinces him to abandon his mission and be at peace. Thanking Yuna, Lenne guides Shuyin's spirit to peace on the Farplane.

Subsequently, the fayth once located in Bevelle appears before Yuna and thanks her as well. He then asks her if she would like to see "him" again. Should the player reply "Yes"—and a sufficient percentage of the game's optional storyline has been completed—the fayth locate Tidus' scattered pyreflies and send them to Besaid, where they reform. But should the player select "Its better this way" you will not get the good or perfect ending even if you do get 100%. Thus, when Yuna returns home, she is reunited with Tidus. Players who achieve 100% completion see an additional reunion scene in Zanarkand.