In chapter 33, it is revealed that Eirin knew very well how much she hurt Rin, and has felt like a monster for all the nine years after her imprisonment. Oh, and Rin is only the latest in the list of Eirin's experiments that have Gone Horribly Wrong. Up until then, she's been a total jerk to everyone, especially Reisen, and of course the Rin Satsuki Experiment is more than enough of a reason to hate her, but damn, you can't help but feel at least a little sorry for her when she says that she's beyond redemption and knows it, and just wants to rescue Kaguya before facing her rightful punishment. Goes to show that even the JerkassMad Scientist has a conscience and could actually have been a decent person if only her passion for her work hadn't always had horrible consequences for everyone around her.
Chapter 45 just makes the above statement even worse when we finally learn the full story. It's all Yuuka's fault for forcing Rin to relive those traumatic memories to see who she's dealing with. To make things worse, forcing herself to turn back to normal after becoming a Blob Monster will actually HURT her and make her cough up blood, practically killing her, and when she's sealed away for 9 years, she doesn't even know when it's her birthday, ever, for NINE YEARS! Poor Rin! D:
Happy birthday to me,
Happy birthday to me,
I don't know if it's my birthday,
But it's passed by now, surely.
From the exchange between Reisin and Sakuya from Chapter 51, after, Sakuya and Remilia have to stay at Reimu's shrine
Reisen: She was a nine year old girl!
Reisen: I dreamed of Rin every night for almost a year after that. I begged Eirin and Princess Kaguya to change their minds so many times that they threatened to send me back to the moon if I didn't stop. What did you do?
Chapter 57. The death of Marisa. Especially heartbreaking when 5 minutes ago she had just defeated Yuuka pretty much singlehandedly, but showed mercy.
Let's Fight Like Gentlemen says Yuuka. But the ending shows there's going to be no honor in the battlefield. Way to break your word Yuuka.
Chapter 58 When Yuuka re-used Marisa's dead body to fight Reimu. While Reimu beg Yuuka to stop that, she just leave the scene while saying "One last... Friendly duel with her"
It's even more Heartbreaking when Reimu step on the Mini-Hakkero: She take it and aim at Marisa's dead body while saying "You wanna do your master one last service?" and then she proceed to recite the Master Spark formula
The moment when Reimu perform the Master Spark:
Reimu could hear Marisa Kirisame ghost voice instruct her to perform her trademark spell
"Aw it's easy! First, concentrate your mind
Reimu look down at the crushed Mini-Hakkero, they both knew what they had to do
"Mutter the spell to the Hakkero"
She wasn't sure how but the Hakkero responded
"Point it at someone you don't like"
Reimu pointed at the person she loved more than anything in the world
"And unleash the power of Love!"
Chapter 59. The last word of Captain Kotohime Sonozika for Marisa's death
"And yet, despite how much i disliked her, despite all the problem she caused and how much i hate that people are treating her death as more important than the people we worked to protect her, she had to go and die..." She swallowed and her eyes were confused "... In the most selfless, noble and heroic way i've ever heard of. Isn't that just the most awful thing, that i'm actually angry with her for not letting me to resent her properly?"
Patchouli's death. She, Sakuya and most of the Komeiji pets go in a suicide mission to rescue Satori and Flandre from Yuuka, but Patchouli is the first casualty. Seconds after her death, Koakuma dissappears, because she was Patchouli's familiar and she was bound to her. And the end of the episode reveals it was Mima disguised as Yukari the one who sent Patchouli and Sakuya on the suicide mission as a Revenge by Proxy on Remilia, whom she blames for Marisa's death.
It was also sad to see Mima standing next to Patchouli's remains as she gloats that she never cared about her and was just using her for the sake of her revenge on Remilia. And to think Patchouli adored Mima and considered herself her biggest fan...