"Darkness of the Unknown," the song that plays during part of the climactic battle with Xemnas at the end of Kingdom Hearts II, is also known as "Duet of the Keyblade Masters," so-named for the perfect harmony exercised by Sora and Riku during the fight.
Despite how easy it would be to attach Sora and Riku's tender moment on the Dark Margin to a title like "Duet of the Keyblade Masters", "Darkness of the Unknown" feels like its significance remains firmly tied to those deemed unworthy of existence. Xemnas's boss music is highly reminiscent of the "13th" series ("Struggle"/"Dilemma"/"Reflection") that is used for the other members of the Organization. Xemnas manipulated them all, using them like the emotionless tools he led them to believe they had become. It seems fitting that his theme, only heard after every other member had been finished off in one way or another, is the culmination of all their final dirges.
Throughout the series, the effects of these manipulations are shown on a variety of characters, particularly Roxas, Axel, and Xion. Several scenes show the trio grappling with orders given to them by the Superior. In one such instance, Axel has to retrieve Xion, who is about to go rogue. As he agonizes over the situation, he is forced to deal with three different ideas of what is "right," coming from Xemnas, Xion, and of course, Axel himself. In the end, he fights Xion and brings her back to the castle, not knowing if he had undone the friendships he had managed to build.