Taking place two years after the events of Final Fantasy X, Final Fantasy X-2 follows the reconstruction of Spira, for better or worse. The story revolves around three young women: the returning characters Yuna of Bevelle and Rikku the Al Bhed, and a new character named Paine.

In a prequel story to this game , Yuna is dealing with the aftermath of having saved the world. The factions flowering in the Eternal Calm all want her support of their ideologies, and she is rudderless now that she has fulfilled her purpose for living and lost her beloved. Rikku arrives with a memory sphere found by Kimahri showing someone very like Tidus in a dark place, being punished. She convinces Yuna that she's done her duty to the world and deserves to follow her heart.

The game is punctuated by Yuna addressing Tidus (as if writing a letter to a distant loved one) with her thoughts and memories of the places they pass through and their own relationship, as she searches for a place in the new world. The main storyline of the game follows the clash of philosphical factions as their struggles uncover some nasty legacies from Spira's ancient history.

A significant portion of the game is unnecessary for completion of the main storyline, but much of the depth of the game is in the optional content, which generally follows how each part of Spira is healing, along with Yuna's search for Tidus. The themes of the game include searching for identity and acceptance of that identity, as well as coming to terms with loss, change, and the limits of personal responsibility. Like other second-time saviors, Yuna comes to reject the notion that sacrifice is the only way to solve problems.