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I started out by watching the anime for Gunslinger Girl, and now I want to finish the story by reading the Manga. On what chapter does the anime end? And does the anime skip or change any chapters?

I guess what I'm really asking is:

What would I need to read, in order to cover the difference between the Anime and the Manga?

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There are no relevant differences between the manga and the first season of the Gunslinger Girl anime, as far as I am aware. However, the manga chapters are ordered different in comparison to the anime. The last anime episode of the first season matches the contents of chapter 8 of the manga, which is about half in the first omnibus-format book release, but following chapters do match contents of earlier anime episodes.

Since I haven't watched the second season of the Gunslinger Girl anime, I just looked up the ending of the anime and compared it with the manga. Since the anime ends in the first confrontation with Pinocchio, it matches chapter 15 of the manga, near the end of the first omnibus-format book release. I cannot say anything in regards to the other second season anime episodes.

My honest recommendation is to read the manga from the first chapter. The order might be a bit different, there might be a bit more background story, and certainly some manga scenes from these first chapters are referenced throughout the progression of the series. All by all, around ~16 chapters will only took you an hour or so, especially since you're familiar with the current setting.

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    spoiler Btw, the second season ends with Pinnochio dead, not with the first confrontation. Unless he's not actually dead somehow? Did I interpret that incorrectly?
    – Kent
    Feb 21, 2014 at 20:00
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    @Builder_K Ah, apologies for the confusion. Indeed, I matched the ending of the second season of the anime series to the completely incorrect chapter (I hurried looking up a bit too much...). Pinocchio does indeed die, and in the manga, that is the end of volume 5. My earlier point still stands though, there is no way that the anime covers everything that happened in 3~3.5 volumes in 13~15 episodes.
    – Deathspike
    Feb 21, 2014 at 21:34

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