Episode 15: "The Seven Emerge". The episode is a bleak portrayal of just how scared to die Gene is, and his first experience of being in way over his head. Threatened by the assassin Shimi, Gene haughtily proclaims that he can easily defeat him. Then he gets his ass handed to him. Repeatedly. During the battle with Shimi, Gene gets shot in the stomach, every member of the crew has a fake-out death, and they only win by sheer dumb luck. It's horrible just how close the Outlaw Star crew came to being utterly annihilated, and it was only that Shimi took pity on them that they escaped alive.
There's also the scene about halfway through the episode where Melfina comes to visit Gene, and, convinced that he's going to die but trying not to show it, he tries to make her sleep with him, which terrifies her. In this case, his lecherousness is not played for laughs. He angrily asks Melfina why she was created, and she starts crying, saying that she doesn't know. It's the first time Gene is faced with what a flawed person he is. Thankfully, he slowly gets better.
Episode 20 "Cats and Girls and Spaceships", where Jim meets Hanmyo and develops a crush on her. Which ends with a grappler ship duel with the Outlaw Star, who wasn't aware the enemy ship was being piloted by a child. So, when Jim heads back to the park afterward. Expecting to meet her for their date, she inevitably doesn't show. Made worse, since Hanmyo hadn't known she was fighting Jim, either.
Hanmyo's horrified reaction to Mata's death in particular is surprisingly heartbreaking. While she was obviously angry over Kemi's death, it seems Mata's death is what finally broke her. Proof that the girl genuinely cared for cats/co-pilots.
Episode 25 "Maze of Despair," Despite how unhinged he's been throughout the series, Harry's death is surprisingly poignant. He fights for Melfina's sake, not even being concerned in her role to get to use the power of the Leyline and to defend her against someone who not only is using her to achieve his selfish ambitions but disregards her autonomy completely. He fights valiantly, but then dies a horrific death as he's forced to acknowledge his inability to be neither her love nor her savior. With his last actions as a physical being, Harry allows Gene to rescue her as a humanizing moment, knowing that Gene despite his own baggage of issues, is the better man for her and the one to rescue her.
While Hitoriga showed himself to be an utterly repugnant killer Suzuka showed disgust over his dismal of his killing of her family and his unhealthy fixation over her. When he finally dies, his deranged experience shows a calming humanity beyond it resembling Suzuka. When he finally falls, it's not satisfaction that she feels but a silent sorrowful expression on her face. It's implied she either pitied how his fixation over her turned him into a pitiful monster she needed to shoot down or Hitoriga meant something more to her as an implied close personal figure in her life and had to put him out of his misery for how disgracefully he fell onto the path of evil.
Equally, Ron's reaction to Harry's near-death is poignant as well and highlights despite them both being unrepentant opportunists and otherwise complete scum who backstab all factions, they do care about one another with Ron being emotionally distraught when Gwen dismisses his distress and Gene barging in.
