If you read my earlier entries on this series, you probably already know a little about it. Jinki: Extend, at its core, isn’t really that incredible. However, the way it’s been written and executed is extremely good, maintaining a sense of mystery and intrigue througout the series. I’ve seen to episode 11, and I know there are some people who have had trouble sorting out exactly what’s going on, so let’s discuss the plot. Consider this a spoiler warning.
First off, a disclaimer. I’d like to point out that there are still some gaps in the plot here, and I’ll explain where they are. Hopefully these gaps will be filled in in the last few episodes, because I absolutely hate being left with questions, and it will kill my opinion of this series, which up until now has been extremely good. Also, this is my interpretation of what was going on so far, and I may make some mistakes.
One of the more confusing aspects of this series is that the action is occurring in two different time periods. Also, there’s some backstory which predates both periods. Let’s call the backstory past, Aoba’s part of the story present, and Akao’s part the future.
The whole plot stems from and revolves around one person. While he’s not introduced until a little way into the series, it’s clear from the start that Hakuya’s the villain. What we eventually find out though is that he’s the reason behind just about everything that has happened in the series. He didn’t always wear the mask. It’s not been explained why he wears a mask, actually, and I suspect it might never be. Anyway, we don’t quite know why it is he was so important, but it seems that he was being raised for a purpose.
The other important figures from the past are Akana and Genta. It seems that Akana was a scientist who worked on the reactor which powers all of the Jinkis. These reactors were hardly mentioned, surprisingly, until later on. Some kind of quasi-magical power supply or something, I expect not unlike the S^2 Engine in Evangelion. Anyway, we don’t know why (yet?) but it seems that Hakuya was being raised by Akana, not unlike the way that Satuki raised Kouse. Hakuya it seems was obsessed with Akana, and when he found out that she was more interested in Genta (clearly due to the facial hair :P) he flipped out and went crazy.
In his despair, it seems that Hakuya raped a girl. While it wasn’t actually mentioned directly, it’s pretty much implicit that she was Satsuki, Aoba’s mother. While the voice doesn’t match, the hair and eye colour does, the relative ages are correct, and it would certainly explain why Aoba herself looked quite similar to Hakuya and Satsuki both. It would also go a long way towards explaining exactly why it is that Satsuki seemed to hate her daughter so much. What ever happened to Satsuki, anyway?
Anyway, the final point in the past which is important is that Hakuya went to kill Genta, and instead ended up killing Akana accidentally. He then cloned her, creating Akao, as some kind of twisted revenge against Genta. This is about where we go into the ‘present’ part of the plot.
I’ve seena lot of people claiming that Aoba is a clone as well, but this just doesn’t make sense for me. I think the confusion comes from the fact that Shiba called both her and Akao similar things, and since Akao is a clone, it seems to follow. But to my way of thinking, this would more likely be something due to Aoba’s father. Anyway, Shiba is sort of a bridge between the present and future time periods - she’s most prevalent in the Future period, but she is a clone of Satsuki. It would seem that the last battle between Aoba and Satsuki and Kouse caused Satsuki to no longer be useful to Hakuya, because she hasn’t been in the series ever since. What happened to her, anyway?
Akao, meanwhile, has no memory of her past. However we know that she was the one who went berserk and killed a whole ton of people - the ‘Lost Life Phenomenon’ which several people mentioned. There’s a bit in here that I just don’t get, the biggest being the way that Shiba and Akao seemed to merge together.
I don’t think there’s much more of the plot left to straighten out. When you put the pieces together, it’s actually not that complex, which just goes to show how well executed the whole thing is. Looking forward to the final two episodes. 
I just didn’t feel involved with the story.
I was to confused to care with how it ended.
Ok, yes, extremely late. But I haven’t been around this part of the Internet in a long while.
And I wanted to point some things out. Sue me. 
The name of Aoba’s mother is Shizuka Tsuzaki, not Satsuki. There’s a Satsuki among the 1991 cast, however.
Indeed, Aoba is not a clone. She is the natural-born daughter of Hakuya/Kokusho and Shizuka.
Finally, for any of you who can read Japanese (since ADV Manga has halted a bunch of their manga titles, including Jinki: Extend), read the manga. I try to spread the word out wherever I go, the manga is much much better than the anime.
If you can, try and convince some scanlators somewhere to do the manga.