The original work are the novels, then came the anime. The anime was based on and was similar to the novels all through season 1 and part of season 2. The end of season 2 and all of season 3 is anime-canon, meaning that the original author wasn't involved.
The manga stayed true (more or less) to the novels up till chapter 96. We don't know exactly why the plot changed. Maybe the Seisakoku arc was too long (the longest of them all), or too dark.
The manga chapters after 96 could be referred to as "the fire box arc" (since they're not in Seisakoku), and it's not like the novels at all. The setting is different, the bad guys aren't bad, and you can just feel the 'happy ending' approaching, whilst with the novels you get a lot of angst, a lot of action, and a lot of complicated stories that intertwine, death and torture (physical and otherwise). Amidst all of that the characters go through terrible ordeals and then grow. The growth is slow but steady. In the manga the growth happens very quickly and without a proper explanation.
Now, I personally like happy endings so I don't mind the manga changes, but it just feels so simple compared to the novels.
Thanks. Yeah, I was wonder why the manga veered from the novels. I prefer the original novels, but I liked the anime, too. And now I like the manga :P it's all good.
So, if I understand correctly, the manga, anime and novels all have slightly different plots. Is that correct? I was hoping the manga would follow the novels, but I'll enjoy KKM whatever the case (▰˘◡˘▰)