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Shounen Ai or Yaoi Implications
Yaoi doujinshi seems to be the most common genre of Kenshin doujinshi there is. Personally, I have absolutely nothing against it, I just don't care for it between the main Kenshin chars. I don't mind light shounen-ai, sometimes I even like it if done tastefully and in-character. Also, as far as yaoi goes, I generally don't like sexually graphic doujinshi of any kind. Either way, since it is so prolific, I did end up with some (some more graphic than others- some nice light shounen-ai) and I've grouped them here. I didn't scan anything bad, and the descriptions I gave aren't graphic, but most importantly, if you don't want to see it, don't look.
Shintaniomakase, by Hysteria (?) Circle, has three stories in it some of them contain some light shonen-ai. The first is about Hiko remembering arguing with little Kenshin. The second, deals with Kenshin's relationships with Hiko and Sano..... The third starts when Kenshin is kicked out of (the only) bed at Hiko's place (Kenshin is wearing the traditional japanese underwear at the time which is pretty much a loin cloth....) and Hiko eventually lets him sleep next to him. It has 34 pages.
Rurouni Kenshin: Meiji Kenkakku Romantan, Circle Unknown. This doujinshi has 31 pages of 3 text stories in addition to the manga-type stories. It has a couple cute pictures with inconsistent artstyles. One of the stories with Sano and Kenshin and Yahiko has a really odd artstyle, though. The last story, right before the longest text story, is a 4 page yaoi with Kenshin and Hiko- it dosn't really show anything, but, well, it's enough to bother me. Another thing I recently noticed in this doujinshi is that it contains a one page feature that I'm pretty sure Watsuki did himself- I'll try to get that pages scanned sometime soon. It has 72 pages.
Sword School Guidebook: Hiten Mitsu Master and Student's Beloved Book; Circle Unknown. Like the cover implies, this doujinshi mainly focuses on Hiko and Kenshin. There was one 2 page rather yaoi story in the middle (though my copy no longer contains it- I really do feel bad about doing that to books, but I liked it other than that page and so as long as I was planning on keeping it I didn't see any reason that I would need to have those pages if I didn't care for them...) Other than that, it has like 2 places with some really light shounen-ai. The first half of the book is composed of a a short or three (one a gag of Misao and Okina- when she finds his ninja outfit gone,) the others about Hiko and Kenshin. The artwork in them is pretty cute. The second half is a big text story. It has 38 pages.
Sazare(ri?); unknown circle. This doujinshi has a couple shorter stories in the begining with one really long story after them. One of the shorter stories is done in the same artstyle as the Kyoto doujinshi (though I have no idea if the circle is the same.) Some of the stories in this doujinshi are either disturbing and dark or have yaoi implications, but the artstyle is generally impressive. They all focus on Hiko and Kenshin. The first short is odd- it appears that Hiko makes a realistic doll of Kenshin and then thrwows it in the kiln to burn. I don't get it. The next to are short and gags. After that is a rather flowery one with little Kenshin and Hiko- the one after that little Kenshin finds a kitten that he tries to convince Hiko to let him keep. After that is the main, long story. It takes place during the Kyot arc and is long and contains the most yaoi implications. Apparently, Hiko pushes his affections on Kenshin (it dosn't really show much at all- but you can get the gist of it.) Meanwhile, Sano runs into Megumi and dosn't "hit" it off with her too well (ie she slaps him.) Sano gets upset and thinks of Kenshin. He goes and finds him at Hiko's shack and can tell something's up. He speaks with Hiko about Kenshin. After that it goes to show Kenshin learning the succession technique- afterwards (and after Hiko's recovered as in the anime) they part on good terms. After Kenshin is gone, apparently Hiko was either much worse injured than indicated or he had tuburculosis, because he coughs up blood, envisions Kenshin, and dies. It has 78 pages.
Datenshi books (I'm not sure if that's actually the circle name or not, have a rounded style and, from what I've seen, often shounen-ai storylines.
Flying Sky; Laughing Fallen Angels circle,Datenshi Book no. 33. This doujinshi has light shounen-ai stories between Sano and Kenshin. I'm not exactly where one story ends and the next begins because the art style is the same all the way through and the plots are relatively similar and there are no obvious markers. For all I know, it may be one large story, but I don't think so. Anway, there's nothing worse than hugging and it's pretty cute. It has 34 pages.
Hiten (Flying Sky) number 37. This is another fairly average Datenshi book. It has the characteristic rounded artstyle with light shounen-ai worked in. It has a few short stories, one has Sano sneaking into Kenshin's room one night to ... come on to him. Another is a fight between Kenshin and Aoshi, but it looks like it has a twist/funny ending that I can't read. The last one is a shonen-ai with Yutaro and Yahiko. It has 34 pages.
Flying Sky #? This doujinshi contains more gag shounen-ai stories than some of the others and is really cute in general. The first story has Misao daydreaming about Aoshi during her travels with Kenshin, Another has a drunk Hiko hitting on Kenshin) until he realizes his mistake that Kenshin isn't a woman. The longest one is one where Sano is messing with Yahiko (I think he thinks he's cute- and freaking out Yahiko at first, but things wrap up nicely. It has 54 pages!
Rintoshyanto(?), "Warau Datenshi book #39), has the same artsyle as the previous book that I have by the same circle. There are a couple short stories, with cameos of characters like Katsu, Yutaro, and Aoshi along with the Kenshingumi. The last two stories have shounen-ai connotations- the first of the two with the strongest (it shows Kenshin and sano lying in bed next to eachother.) The artstyle, though, keeps it very clean. The second of the two just has them doing a lot of talking. The doujinshi has 26 pages.
Meeting (kanji) bishonen-4 (?), unknown circle. There are a couple short and one long stories in this doujinshi. The shorts include one with Hiko and Aoshi in modern clothes, and one gag with Kaoru, Misao, Hiko and Aoshi. The long one is a shounen-ai between Kenshin and Sano. It dosn't go beyond kissing, but I still don't care for the way that It is presented. The artstyle in the dounjinshi is generally pretty sketchy and a little bit off, but not bad. In my opinion, the best part of the doujinshi is some really nice full page character pictures in the back of Kenshin, Hiko, Sano, Aoshi, and Sagara. It has 40 pages.
Tokyo Romantan vol. 9, Keep Faith- Alliance. There are 3 stories in this doujinshi. The first one is a light shounen-ai between Kenshin and Sano on a ship, and is actually pretty sweet. The second is another Kenshin and Sano shounen-ai- this one back at the dojo. Both stories are well-drawn and have nothing worse than a peck on the forehead/cheek. The last story, which is on a red paper, is a short, dramatic story with Kenshin, Enishi, and Tomoe. It looks really neat and the artstyle works well with it. It has 54 pages.
Aka- on the back inside cover it says Airi Tojo; Dolce. This is a fairly random, though pretty well drawn shounen-ai between Kenshin and Sano. It does skip to later in the story when it looks like something was about to happen- which is good in my opinion. There really isn't that much else to say about it. It has 30 pages.
Ka Ren- unknown circle. This doujinshi is pretty short with not too much content. The main part of the doujinshi is a 10 page shounen-ai story between Kenshin and Sano, which is drawn pretty nicely, but even with only ten pages, a couple of the pages manage not to have any of the caracters on them. The very first page is a cute couple of drawings of a chibi-neko Kenshin (the page I scanned.) Other than that, there are 2 drawings of the faces of Yahiko and Yutaro on the author's comment pages and a nice picture of Kenshin advertising the next edition. It has 22 pages.
Rurouni de Gozaru by MIG21SP (?) When my boyfriend went to California (and thus to some of the nice, big anime stores there) I asked him to look for Kenshin doujinshi for me- specifically non-yaoi doujinshi. He decided not to look too closely at what he bought, so this doujinshi (and the next one) are a result of this (though how he couldn't tell by looking at the covers is beyond me.) This one isn't that bad- as in it's not graphic, but it is blatantly yaoi. Then in the middle of it there is an odd flashback to when Kenshin was hitokiri, but he looks VERY feminine in the flashback. *shrugs* This doujinshi has been sold. Anyway, it has 26 pages.
Utakata, unknown circle. This doujinshi, another 'gift' from my not-too-observant boyfriend, is, quite simply, yaoi. (sigh- it says on the cover (Kenshin x Sanosuke) even though it is in Japanese, he should have known enough to identify that...) Erm.. the artwork is alright, I guess- though... the subject is not to my liking. From what I've seen while quickly flipping through it (very quickly) it is decently graphic, though avoids really showing anything. Pages 8-17 are a text story. The rest is manga-style. This doujinshi is No longer in my possession. It has 42 pages.
Hiiro no Ken (Red-colored sword?), an anthology by various circles. I just recently got this doujinshi from ebay ( I finally broke down and bought some doujinshi from the states- I couldn't wait any longer.) There are quite a few selections by various circles in this anthology, and a large portion of them contain yaoi hints- some of them more than hints. The artwork generally varies, but is overall pretty decent. The cover is also just adorable (which is what really made me bid for it.) Some of the stories include one where Kenshin and Sano are in the Oniwabanshu (with some really cute SD's), a really bizarre one where Kenshin has a nightmare that Sano is a woman and Kaoru is a rather ugly man, one with Kenshin flashbacking to his battousai days, some that don't particularly stand out story-wise from just the illustrations but have some cute artwork, some mediocre ones, and a decently graphic yaoi story. It has 240 pages.
Tokyo Romantan by Ren Mizumori with Pandora's Box. This doujinshi has a sketchy, angular, but cute artstyle. In it, Kenshin has gone off with Sano to do some errands and they stop by the riverside on the way back to rest. There, Sano gives Kenshin a Kiss and a big hug- Kenshin panicks but quickly recovers and they walk home together happy. It's short, but cute in a shiny-happy kinda way. It has 22 pages.

Ake no (something) by Fujimori Miki. The artstyle in this doujinshi is incredibly pretty- and one of the most interesting things about it is the full-page shots of the characters in the back of it. Each picture features 2 images of a character- the normal version and then either an older or younger version of them, depending on how old they are in the anime. The story itself is fairly generic for shounen-ai Kenshin stories from what I can tell. The Kenshin gumi are out shopping, and as soon as Kaoru and Yahiko wander off, Kenshin and Sano sneak a kiss. When the Kenshingumi's photo is taken later, Kenshin and Sano are giving eachother significant looks. It has 30 pages.

Shesuta (?) by unknown circle. This doujinshi also has some really pretty illustrations. It has several short stories. In one, Yahiko finds a kitten (this seems to be a very common theme in doujinshi.) Another has a flashback story to when Sano was in the Sekihoutai. In the third, Kenshin is cleaning his sword in the dojo when someone from his past suddenly shows up. Apparently this man had a relationship with him when Kenshin was the Battousai. The last one is has a really sketchy artstlye and has Kenshin washing himself when Sano comes up behind him to kiss him. It has 50 pages.

Hananoen by Gekkohyoko. This is a thick doujinshi with many short stories and full-page character pictures interspaced with what looks like information about different doujinshi I'm guessing that this circle has put out. The next to last story is the longest and it is a shounen-ai story between Sano and Kenshin where Kenshin is staying at Sano's place and they end up talking for a while and bonding. It has 80 pages.
Hanazange Kuchinashi. This is a very short, nicely drawn doujinshi that is pretty straight to the point. Kenshin and Sano are both feeling down. Sano walks up to Kenshin, they talk, they kiss and the doujinshi ends. It has 22 pages.
More shounen Ai/Yaoi on Page 2