Another great story here. I especially liked the class president's part. If it isn't sexual for the girl, it only makes it look more casual, and as a result quite sexy for someone who enjoys casual guro, like me.

And if you're taking request I can't miss the chance to suggest... dramatic pause... Ayanami Rei! ... .... ... Huh? No one is surprised? Oh, well.
If you want a premice, I can think of a couple of them.

First is like that: JSSDF succesfully captures NERV HQ and kills all the staff on sight, except the EVA pilots. The pilots did save the humanity from Angels after all, so they deserve an honorable death by seppuku. Rei, complying without hesitation, most probably goes first. Then Asuka, who probably complains a lot about how she's not even fully Japanese, but still she goes for it, as she doesn't want to look like she's afraid of it. Finally, Shinji, who probably served as the second for the girls. He isn't in a relationship with either of them, but clearly attracted to both of them. So he properly enjoys the show. In the end though there's no second for him, so Shinji has to die slowly in pain, but he is comforted by the thought that he has witnessed such a sexy show as two girls he liked committing seppuku, and he might also like hug their bodies and heads as he dies or something. There migth also be a funny moment when Shinji first tries to cut Rei's head, but fails, either applying to little force so that the sword doesn't go all the way through the neck, or missing the neck and cutting deep into Rei's shoulder or something. Shinji's like "oh, sorry", and for Rei it hurts of course, but still she's like "it's okay, just try again". Or it might be the opposite with Shinji having a lot of skill in swordsmanship from piloting EVA and can make a perfect cut almost through the neck, but not entirely, so that Rei's head is left hanging on a little piece of skin. Anyway, the details are up to you, the only part I really care about is Rei obediently committing seppuku, as it doesn't even occur to her to have any regrets or something. The other parts are not important, like if you don't want to write a male seppuku, feel free to make a twist that saves Shinji's life in the end. Or maybe he wasn't captured in the first place. Maybe as cold their relationships were, Gendou made a way for Shinji to escape. So when Rei and Asuka are captured and forced to commit seppuku, Asuka decides to go first so that Rei can be her second. And Rei agrees, seeing no problem in not having a second for herself, as not having a second does not contradict the order to commit seppuku. The premice with pilots being captured sounds dark, but there is no reason to make the story dark: Rei doesn't mind being ordered to die in the first place, Asuka might complain a lot, but still goes for it to prove her courage or something like that. Also, the pilots are likely captured while wearing their plug suits, but as they proceed to seppuku it is in the way, so they have to take it off, which results in them being totally naked.

In case it still dounds too dark and serious, I have a second idea is more casual and random. Shinji, Rei and Asuka are all sexfriends. Shinji has a lot of sex with both girs, they with each other, and they have threesomes too. At some point though Shinji thinks of adding some more spice to the sex. An idea comes to him to have one girl commit seppuku and have sex with the other while watching. But he wonders which should be which? After some thnking Shinji decides: sex with each of the girls is equally fun, even if it might be diferent ways of fun, but the one he truly loves is Rei. So seeing her commit sepuku will be more sensual than seeing Asuka do it, who is only a friend for him. Shinji tells his idea to the girls, he tells Rei should be the one to commit seppuku, but doesn't elaborate why, as he doesn't want to make Asuka jealous and angry, which would result in her not taking part in it, and while Shinji would still enjy seein Rei's seppuku, it would be more fun together with a friend. So then they proceed with the plan, Rei commits seppuku while Shinji and Asuka are watching and having sex, there's no one to cut her head off, instead Shinji and Asuka proceed to playing with Rei's intestines, like pulling them out, masturbating with them, wrapping them around their bodies and so on, all while Rei is still alive. And of course they all three have a lot of fun and no regrets.