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Tear Jerker: In Flight
Matsu gets punished by being scolded and losing her place from sitting and sleeping with Shirou for bringing up more of his past that he wanted. Disproportionate Retribution much?
Absolutely not, it was a really stupid Batman Gambit on her part. But it is still heart breaking for her and for us to see the gentle Shirou erasing her name from the whiteboard.
Somewhat of a Tearjerker on both sides, as the whole situation ended up having Haruka (A nice guy just trying to look out for Kuno's well being), Yukari and Shiina leaving the relative safety of Izumo as a direct consequence. If not for the Bombshells Matsu poked until they went off, they might still be somewhat safe at Izumo. Think about it, not just from how bad it was for Matsu, but how bad it was for Shirou as well.
Maybe to us its not a big deal, but to Sekirei who believe in forever and after more adamently than any other being out there, something like this is pretty harsh. Again, for a Sekirei.
Shirou's revelation that Musubi is in her own way just as distorted as he is.
Thirty-Sixth Wing. We know Shirou can be cold hearted, but to see him plan on losing his sister and the fact that he hates himself over it really just drives home the point of how bad the Path of the Shura is.
Thirty-Eighth Wing. The rift between Shirou and his Mother after she learns who his adoptive father was.
The unexpected conversation with Yasaka. Shirou and Homura know they will never see him again if they follow Shirou's plan.
Shirou (thinking): And that was the crux of Rin: her pride. Her pride as a magus, her pride as a person; even if she couldn't go back to the Clock Tower, even if she had nowhere else to go that didn't mean she would join this group. For Rin, the Clock Tower had been a part of her life, the resources there the only thing that would allow her to progress as a magus. Without it, her magecraft would suffer. Even her lineage was at risk now. Even if she had a child to pass her Crest on to, there would be no guarantee that the Clock Tower would allow it. They would take it on even the off chance that it was part of the preservation of Saber, thus effectively ending the Tousaka line. Just like the Archibald, Rin's heritage would be ended.
Shirou (thinking): Even though joining up with my flock would help keep her alive and her magic safe, if staying with me meant she would have to bend her pride, then she would leave.
Forty-First Wing. The end of the duel against Rin and Saber. Shirou wins, however...