- Even with his Big Bad status, it's not hard to feel sorry for Mandrake's anguish cries after his son's death. Bad guy or good guy, losing a child is never easy.
- The distant relationship between MK and her father, even to the point when she tells him she'll be going through the 5 stages of grief alone.
- Ronin's last moments with Queen Tara.
- A happy one that parallels the above: Ronin's smile when he sees Tara, for a moment, before she chooses her heir.
- Professor Bomba breaking down after he thinks he imagines his daughter as a Leafman.
- This line
Ronin: (when they are entering the Boggan's stronghold, Wrathwood) "I've been here before; with your father."Nod: ") He never told me about this."Ronin: "(Sadly) He never got the chance..."(Nod lets it sink in.)
- Ronin's apparent death in Wrathwood. Almost nothing is said about it, making it all the more painful, especially if you realize that, as far as he knows, Nod just lost the only father figure he's had for most of his life. MK's silent understanding (what with her mother's death) makes it all the worse; she clearly knows there's nothing she can say to make it better. Finn's face says the same thing when he understands what Nod means...
- After the climax of the film, the human-sized MK and reunites with her dad. He is looking over an old picture of their family and manages to choke out only part of a heartbreaking sentence:
Professor Bomba: I always hoped if I uh... if I proved it to her, she'd uh... you know...
- The fact that the movie, despite being exciting and funny, can be quite morbid too. It has several deaths.
- The whole reason MK is moving is because her mother died. Having a parent die is very sad.
- Queen Tara, one of the friendliest characters, dying.
- Seeing a fruit fly child grow up, grow old and die in a minute. It was Played for Laughs, but still.
- Seeing the bat that Mandrake shot die. We know it's dead 'cause there's a skeleton.
- When Bomba suspects MK's turtle to be dead. note
Bomba: "We got your dolls, your pictures, your turtle—oh, dear."