- Ledo recalling the fate of his brother in episode 4, in which we see why he was absentmindedly carving that flute. This comes after he'd spent the majority of the episode mystified at the concept of family and musing over how inefficient it is for Gargantia to allow weak-bodied individuals to live. The tragic irony hits once you realize that his brother was likely one of those very sorts of individuals.
- Episode 7, Ledo leaves the ship in frustration, leaving Amy heartbroken just one episode after the dance.
- A double whammy in episode 8. Captain Fairlock dies of a sudden heart attack, leaving Ridget in charge of Gargantia. We see that underneath her cool, stuffy exterior she's still a nervous 22-year-old who needs her people as much as they need her. Then Ledo states that he has to fight the Hideauze/Whalesquids...but not just because the Alliance programmed him to do so, but because he wants to protect Amy and Bevel and keep Gargantia from becoming like the Alliance. Meanwhile Amy breaks down crying, claiming that Ledo was so close to regaining his humanity. Whether you agree more with Ledo or Gargantia's view, it's all still quite heart-rending.
- The origins of the Hideauze and the Alliance, and the truth of Earth's past. Either mankind had to doom the planet to do the right thing, or live in peace by accepting great evil. The situation tore the world apart, and we get to see the world slowly burn from the point of view of news networks and archive footage.
- Chamber's Heroic Sacrifice in the finale.
- Ledo being left in tears when he realizes what Chamber did for him.
- The second OVA shows Kugel's Start of Darkness when his Love Interest Linaria succumbs to her illness. After spending time on her deathbed thanking Kugel for all that he did for her and her fleet, Kugel takes her up to the top of the fleet, with nothing but beautiful blue oceans surrounding the ships. This is the last thing Linaria ever sees before her death. Kugel then breaks down, wondering why he can't even save one girl when everyone else is worshiping him as a divine emissary.
- Also a brief scene of Kugel adopting Linaria's pet squirrel after her death.
- Heck the whole OVA is this. It turns out Kugel was Not So Different from Ledo. In fact he was genuinely a good person who was trying his best to help all the people of his fleet. After Linaria's death, Striker prodded him into becoming a Fallen Hero. If they had landed in different places Ledo could have easily ended up like Kugel, and vice versa.
Tear Jerker / Gargantia on the Verdurous Planet