The story of Birth by Sleep can be a tricky one to follow. The separation of characters makes it somewhat difficult to figure out how things line up chronologically.
It all starts the day of the Mark of Mastery Exam. Terra and Aqua are competing for the rank of Keyblade Master, and Master Xehanort has traveled a long way to watch over the examinations. Ventus watches from the sidelines as the exam carries on, but when things take an unexpected turn for the worse, he’s forced to join Terra and Aqua in the fight. When all is said and done, only Aqua emerges a master, as Terra’s heart temporarily opened to darkness in an effort to gain the upper hand during the exam.
Meanwhile, a strange new enemy, the Unversed, emerges in each of the many worlds. Master Eraqus assigns Terra and Aqua to go out and take care of this threat, as well as find Master Xehanort, who has also gone missing. Elsewhere, a mysterious masked boy coaxes Ventus into following Terra away from home. Terra, Ventus, and Aqua travel to many worlds, not meeting again until they arrive at a place called Radiant Garden.
The three of them work together to take down a powerful Unversed, but then things start to fall apart. Aqua has been asked to bring Ventus home, as well as keep an eye on Terra, whose heart continues to fall deeper and deeper into darkness with each new world he visits. Ventus explains that he can’t go home until he finds the masked boy, who Terra recognizes as Vanitas, the one who threatens to upset the balance of light and darkness in the worlds. The three of them go their separate ways again, each uncovering more and more behind the mystery of the Unversed, Vanitas, and Master Xehanort’s disappearance.
When the truth is uncovered, the three friends travel to the ancient Keyblade Graveyard for the final battles that await them.