At Journey's End. Many players love this Nonstandard Game Over even though it leads to a bad ending. Raynie's Love Epiphany is awkward, the conditions for her Romance Sidequest are ridiculous and nonsensical, and Stocke showed no romantic interest prior, but seeing her give Stocke The Glomp in the bad end, and seeing Stocke make The Promise in the correct response, makes the whole thing worth it. It's the only moment they show affection for each other.
That and people think it's hilarious and awesome that Stocke would just give up fighting to be with Raynie for a year and go back to Historia where Teo and Lippti gently give him a What the Hell, Hero?
Speaking of which, Raynie's ending cutscene if you complete that quest. Marco and the rest of their squad are in the bar in Alistel, celebrating, but Raynie is standing outside by the signboard. Marco goes out to ask her why, and she flashes back to a moment earlier in the game when she was waiting for Stocke there to make sure he could find them. She tells Marco that if she doesn't wait, how will Stocke know where to look for them when he comes back? Becomes an absolute Tear Jerker if you don't get the true ending, though.
On their first mission together, Stocke is somewhat cold and aloof to his new subordinates, making most of their attempts at conversation somewhat awkward. After Raynie and Marco die, Stocke barely escapes. Wounded and unconscious, Stocke is taken to Historia, where Teo and Lippti explain that he can use the White Chronicle to relive past events and shape a "true history." Stocke is understandably skeptical, but he soon realizes that the twins are basically offering him the ability to bend time to his will. Anything is within his power. But then:
Lippti: If that is what is meant to occur, then...Yes.
Stocke: ...Raynie...Marco...it won't be long now. I'll save you both!
Throughout the rest of the game, Stocke slowly pulls further from his shell, accumulating a strong group of Nakama towards which he is completely dedicated, heart and soul. And they feel the same way, showing time and again their faith in and loyalty towards him. The story is riddled with small moments of heartwarming that underscore his ongoing character development, but things snowball near the end, when he discovers that in order to stop the desertification, he must sacrifice himself as part of the Ritual. Earlier in the story, Stocke unwaveringly denounced said Ritual as unjustifiable and repugnant, but by the climax of the game, he is so completely dedicated to sparing his friends and humanity from more suffering, even if only for a time, that he immediately decides to take part in the Ritual upon discovering his identity as Ernst. It really highlights just how far he's come—from Not So Stoic to Messianic Archetype.
This is made even better (or worse) by the You Are Not Alone moment that comes just before Stocke sacrifices himself. At this point, everyone in his party is completely dedicated to him, and some break down completely, begging him not to leave them behind. Even when they accept his choice, they all tell him that they are always with him, and that they fully expect him to come back someday.
In the two "Final" chapters, as mentioned above, Stocke discovers his role, and that of every White Chronicle bearer before him, as a Sacrifice in the Ritual to preserve humanity. Teo and Lippti, of course, knew all about this, as they are the guardians of Historia as well as overseers of the Ritual in the several hundred years since the fall of the Empire. As Stocke prepares himself for his final confrontation, the twins appear. Lippti sincerely apologizes for having hid the truth from him, but Stocke, showing just how far he's come, tells her that he's absolutely fine with the way things turned out—after all, he's going to win the impending final battle. Teo agrees, then tells Stocke that he is proud to have met him, and thanks him for everything he's done.
Everything about the True Ending. Every party member gets an expanded ending that shows just how far they've come, and just how dedicated they are to Stocke's memory. The real kicker, though, comes at the very end. Stocke comes to Historia one last time, where Heiss waits. The two have a long conversation, and acknowledge their relationship as uncle and nephew—perhaps even as close as father and son. Stocke thanks Heiss for giving him a life worth Sacrificing. Heiss is silent as Teo and Lippti appear, ready to initiate the Ritual, but then...
Heiss: No! Not yet!
Stocke: You can't possibly mean to fight me again!
Heiss: No! I won't give up, not on this! *Turns to face Teo and Lippti.* Here, dogs of the Chronicle! Let the world feast on my soul!
Teo: Stop this, Heiss. Your soul has not been prepared as a Sacrifice. A Sacrifice that isn't spiritually awakened won't be able to save the world...
Heiss: Bah...to hell with your "spiritual awakenings"...I know what I want...I just want to see it...The world you'd give yourself to create, my dear boy Ernst...
Heiss: He is the only hope left in the world...If I can't protect that hope, then what other use is my life?