Face-Heel Turn: He arrived to the past years before Natsuki, was taken in by the nobleman Terazawa Katataka and became their retainer - as well as a prosecutor of Christians, and the one who killed Shirou. Therefore, when Natsuki finds him, his mental/emotional state is... not pretty.
Heel-Face Turn: Returns to the side of good gradually, after Natsuki has a chance to get to him.
Genre Savvy - The Strategist: Her most powerful weapons are her historical knowledge and analytical mind. She's said to actually be the most booksmart girl in the whole Japan, and it shows through her encyclopedic knowledge about the Rebellion.
Big Damn Heroes: In the Unzen valley, when a bunch of Christians were going to be tortured to death with boiling water, he uses a trick to make their captors believe that a red dragon had risen from the water.
Heroic BSOD: Almost suffers one when he learns that word of his and Kichou's relationship has leaked and that's why she was imprisoned.
Sex Slave: Became this to Naozumi, after being captured. According to Naozumi, Shirou never yielded to him: he first attempted to understand his "lord"'s broken psyche and then to use this to try helping both Naozumi and his fellow Christians... but when Naozumi realized that he was falling for Shirou, he was so shaken that he strangled the poor dude to death, and then threw his lifeless body into the sea.
High-Class Call Girl - The Mistress: She's referred to as "the prostitute of the castle" as despite her great beauty Kichou actually was an "aishou", a lord's lover in a lower rank than legal wives and prostitutes.
Rescue Romance: Genderflipped: she's the one who saved the amnesiac Miyamoto
Defiant Captive: She's heavily pregnant and gets tossed in a water prison for being a Christian. She refuses to give in, and when Kichou hesitates due to her worry for her, Yone tells her not to rat out Natsuki and Co.
Expy: She plays the in-story role of the real life pregnant peasant whose imprisonment kicked off the whole Shimabara rebellion. Only that, in the story itself, Yone wasn't alone in there: Kichou was thrown in as well.