In a message written to commemorate the game's release, series creator Tetsuya Nomura revealed that he had wanted to make a game exploring Xehanort's past for many years by that point, but the idea had been shelved because it "never fitted what our team wanted." He was eventually able to revisit the idea after the team behind Kingdom Hearts Union χ expressed interest in making a parallel game with a new protagonist, partially helped by the unexpected popularity of the character. Nomura even went as far as to claim that "it all came together like it was destined to be. I do tend to believe in destiny."

In the original version of the "Child of Destiny" epilogue cutscene, Xehanort is referred to as the great-great-grandson of a renowned Keyblade wielder (later revealed to be Spoiler:Ephemer), and the cloaked figure's flashback reveals that they are Spoiler:the player character from Kingdom Hearts χ and Kingdom Hearts Union χ, with the default male appearance being fully visible alongside Ephemer. These were both changed in the version 5.0.1 update, where Xehanort is instead stated to "share a bloodline" with a renowned Keyblade wielder, and the flashback only depicts Spoiler:the player character's arm reaching up to Ephemer's.