Unmarked spoilers are ahead, per Spoilers Off rule.
The first time Jonathan is abused by Captain Continental and refuses his advances, he returns to his room. While he lays in bed Jonathan thinks to himself, “At least the Apocalypse don’t take our dignity.”. He is clearly upset and disturbed about what happened, but he stews in silence as he thinks Leonard is asleep. Leonard however is not asleep and silently observes Jonathan with obvious concern. Neither however say anything to each other about what happened.
The reveal of what happened to Leonard’s little brother. They were both flying a ship when the hull was breached. Leonard was able to secure himself but his brother was not, and Leonard could only hang on to his brother’s hand as the vacuum of space tried to suck him out. Despite Leonard’s best efforts he could not save his brother, and the last image he ever had of his little brother was him being sucked out of the ship screaming, “Nii-san! Nii-san!”
The Downer Ending where Jonathan is forced to Mercy Kill Leonard to prevent him from spending the rest of his life as a killing machine. We then see Jonathan with blank white eyes with tears running down his face, leaving the implication that he's crossed the Despair Event Horizon, which only further adds to the tearjerker levels. The scene is then followed by a sad but beautiful ending theme by Shinichi Ishihara.
