In the manga (manga! manga! not the anime!), everyone returns to Tokyo and everything seems fine, though Sano and Tae note a bit of tension between Kenshin and Kaoru. However, after a night of drinking, the Akabeko is destroyed; attacks are also levelled against the police chief, and a dojo (not in the anime) where Kenshin had spent some time and where Kaoru and Yahiko trained. As Kenshin tries to work out what's going on, everyone's favorite psychobunny Enishi (like Dilandau, only more so) makes an appearance, yells at Kenshin about his nee-san, and talks about Jinchuu (Vengeance of Man, I believe) some more without ever making clear exactly what he means.
Kenshin stumbles home, is greeted with absolutely no pressure and plenty of understanding from Kaoru, and finally realizes he has to tell his friends about his past. (This long flashback, incidentally, appears in the OVA you may have heard of. The manga version is slightly different, but this parenthetical note is getting long enough as it is.) As we all know, he was the Hitokiri, fighting to usher in the new era, etc... he tells of receiving the first half of his cross scar from a young guy, desperate to live and apparently very much in love with his fiancee. Battousai killed him, of course, but the guy lasted a while on pure spirit. Flash forward a bit, and he fights (and kills, of course) some assassins in front of a beautiful young drunk woman who passes out before he can decide what to do about her. So he carts her home and leaves her in the care of the housekeeper. The girl, of course, is Tomoe, and she promptly starts helping with the chores around the place. (Sure, she SEEMS like just a nice, helpful, housewifey sort, but really she's an evil evil woman, wanting to get revenge on my poor Kenshin for killing her fiance. Who was, of course, the guy I mentioned earlier. So unreasonable of her.) Most of Kenshin's comrades-in-arms think she's his girlfriend, and he doesn't take teasing very well. There seems to be a traitor in the ranks who's given away the fact that Kenshin exists... the group is betrayed and has to scatter... and in the scattering, Kenshin and Tomoe go into hiding together. It's suggested they pose as a married couple, but Kenshin would prefer that they not just pose. So they get married, live in the countryside for a while, until Tomoe is taken hostage by the group she'd gone to for help in getting revenge. She was told to discover Battousai's weakness, but the idea was for her to become his weakness, and it's worked. (At some point in here, young Enishi has turned up -- still scary, still fixated on Nee-san, but not QUITE as deranged.) Kenshin goes to rescue her, but he's having problems. Tomoe can see that and moves to protect him, armed only with a knife, but the fool moved in as Kenshin was charging... and his slash hits her as well as his real target. Her death's just that much more of a waste - he would have hit the guy anyway. Her dagger flies from her hand and hits him, forming the other half of the cross scar, and she dies in his arms, smiling.
Enishi can't see that, of course. To him, it looks like his hated enemy, who's been molesting his sister for the past half year and making her do housework for him, has just murdered her. His hair turns white, he goes completely insane, etc.... Back in the present, Kenshin tells what he did once he ceased being the Hitokiri, mentions his discovery that he did kill Tomoe's fiance, and ends his story, leaving the whole group in stunned silence. Talking about it at night, Kaoru says that she "won't die," because it would just hurt Kenshin more; Megumi (kill the fox-bitch!) tells Kaoru she's not a replacement for Tomoe. (Okay, okay, so MAYBE she's saying that the situations are different. Tsubame-chan still seems to agree with me that Megumi was out of line.) The next day, Kaoru shows Yahiko the Kamiya Kasshin Ryu succession technique, and thinks of having Misao bring Tomoe's diary to Tokyo in hopes of using it to stop Enishi. She may not get to fight much, but I think she's smarter in the manga.
Kenshin, meanwhile, has wandered off... she has to go to find him, and they begin philosophizing about how everything changes, moves on... and Kaoru blurts out that she wants to stay with Kenshin forever. After a long pause, Kaoru breaks the silence by laughing and babbling, embarrassed, but Kenshin stops her with an arm around her shoulders and tells her that he'd never had a home, in his years as a rurouni, till now. ^_^
And then, I guess, it's best just to take a long coffee break and then go back, because the mood totally changes, Saitou returns... eh. Saitou's cool, but his mere existence doesn't make me misty-eyed like that last scene did. It is, however, sort of a plot-building thing; Saitou's got a stake in looking for Enishi, etc. We go forward a couple of days. Enishi and company attack, leading into several chapters' worth of fighting, and ONCE AGAIN Yahiko is treated as a better fighter than Kaoru (grrrmuttergrr.) The henchpeople are defeated, so Enishi himself comes down (literally... he was in a hot-air balloon) to fight Kenshin. As this happens, there's a cool scene in which Saitou advises Kaoru that, as Kenshin's weak point, she'd best get out of here now for her own sake and his, because if the fight goes badly for Kenshin, she'll be targeted. She acknowledges this, but says she can't leave and disrupt the fight. Which is still going on, and I have a hard time following it, reading as I am from summaries. But once he's sufficiently beaten the tar out of my baby, he starts making moving threateningly towards Kaoru, speaking mockingly to Kenshin of his Jinchuu, as Kenshin struggles to get away from yet another patented Giant Watsuki Freak (this one bearing a suspicious resemblance to Apocalypse, from the X-Men.) Freed by Saitou and Sano, Kenshin sprints for the dojo, only to collapse, sobbing Kaoru's name (and in the end, dropping the -dono.) We see her lifeless body, pinned to the wall by Enishi's sword, and with a cross scar marked on her cheek.