The third volume, when Setsuna flies in his dream to meet Kira and recalls his previous lives' memories, realizing that he was always waiting for Kira. Kira teases him about forgetting about him, but tells him that he should not return to Tokyo and just remain wherever he is hiding happily with Sara. Couples as a Tear Jerker, too, even in-universe.
The final volume was enough to leave the most stone-hearted reader holding back tears. After 20 volumes of betrayal, pain, rejection, death, heartbreak, psychological damage, and quite literally going through hell and back again, it would have been simply sadistic to give us an ending without our star-crossed lovers reunited. It feels as though this journey to protect the entire world has taken years, but it is all healed in an instant asSetsuna holds Sara in his arms again, just daring to be happy. In fact, this manga was overflowing with lip-quivering, 'awww'-inducing moments.
Watch it, there's some Moral Guardians that would get you for considering any instance of incest 'awww'-worthy.
The ending is made even better when you find out that Kaori Yuki considered giving the series a Downer Ending, but in the end she was too attached to the characters to do such a thing to them.
Kato Yue after fighting his way up from being a worthless delinquent to lost soul, then a guardian, then a champion of the Messiah, to finally managing to lay a blow on Lucifer himself on the day of Apocalypse, finally, finally gets the acknowledgement of the one person he loves most. "You fought well".