Wolverine returns to Japan and learns that The Hand have taken both his adopted daughter Amiko and her guardian Yukio. The Hand are brainwashing Amiko to become a Hand member and eventually turn on her adoptive father.
Wolverine frees them.
It’s implied at the end that Amiko wants to learn to be a ninja–but it’s not clear whether she’s been successfully brainwashed into wanting to kill Wolverine, or if she just admires her father figure and wants to be able to handle herself the way he can.
Yeah, there’s more. Ins-and-outs about The Hand and the Yakuza, but for that kind of detail you should read the books yourself. It’s a fine tale for those who enjoy Wolverine-vs-Hand stories. I liked it, I just don’t see that the details matter all that much.