Marin's fear of darkness and being corrupted, which only gets worse when the solar eclipse happens and she says unkind things to Urin.
Kanon's fear of being rejected by Kojima, to the point where she won't even admit she likes him out of fear.
Urin's fear that Marin will forget about her in favor of being with Kanon, especially since the two of them have to save the world from Sedna.
The entire second half of the show, particularly scenes involving Marin and Urin and how Sedna corrupts Urin to try and make her hate Marin.
Sedna's brainwashing of Urin involves convincing her that no one will come for her, no one will love her, and that it's better to shut down rather than feel anything—by allowing Sedna to inhabit her, she would be released from all sorrow. Not only is it an awful thing to do to someone, it's also what many may feel when in a state of severe depression—feeling unloved and wanting to shut down rather than feel anything.
Episode 8 has a heartbreaking flashback of Marin and Urin as children, as the last scene of the previous episode had a corrupted Urin blasting everyone away and becoming Sedna's vessel.
Episode 8 has Oshima's situation. What initially seems to be your classic Alpha Bitch has heartbreaking hidden depths, as she tells Kanon that even when she was going out with Kojima, all he ever talked about was Kanon. She feels she'll never measure up to Kanon in his eyes, and that it hurts to like someone that much knowing they'll never feel the same way about you.
In episode 9, Kanon realizes that it was her own insecurity that made her feel like Kojima was going to dump her, when in fact he had liked her all along. At the same time, Kojima confesses to Marin that he had liked Kanon from the start, but felt she was purposely separating herself from him, and so they grew distant. However, he feels that when things work out, he'll be able to see Knaon's smile again. Kanon realizes that she never told anyone she liked them out loud even once, and just as she's about to find Kojima and tell him she likes him back, two of Sedna's soldiers capture and nearly kill him.
At the end of episode 11, Marin and Kanon are sprawled on the sea floor as Sedna's darkness flows into them. Then they recognize the darkness as all of the sorrow they and the islanders threw into the sea, and we see a montage of everyone and every kind of sadness it pertained to set to heartbreaking music.
Sorrow of being unable to tell others one's feelings. Sorrow of separation. Sorrow of being unable to understand each other. Countless sorrows...
Even worse is when we see Oshima and Miyako crying their hearts out and Kanon comments that her mother never cried in front of her even after her father died.
In the final episode, Urin begs Marin to hate her so she won't die when Sedna releases her power. Marin responds that nothing could ever make her hate her sister, and doing so would be the most painful thing in the world. It's set to this music.
The last episode. Urin is freed from Sedna's influence and the endless cycle is broken, but Marin and Kanon must separate.
It also has a very convincing Redemption Equals Death as Urin nearly sacrifices herself to stop Sedna and atone for her actions.
The last shot of the last episode is "I'll love you forever." on a blank screen.
The aesop of the series. Everyone has darkness in their hearts. That's okay, and we must learn to accept it, not cast it out.