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Is there any difference between the authentic .hack//SIGN that was made for Japan and the version that was licensed in America in terms of substance or plot? If so, what are some of them? I'd really appreciate it if I could get the testimony of some people who have seen both versions of it.

You mean between the dub and the sub? Because there are some really weird random "rephrasings" that the dub came up with. Otherwise the sub story should be pretty much the same.

Your definition on color of red such as Scarlet and Crimson just like how the simularities of blue being Azure and Cobalt was dealt.

I'm not talking about the difference between the sub and dub. What I am talking about are things like cutting scenes, editting images, cutting or changing dialogue (subs), etc...

S1lentOp wrote:I'm not talking about the difference between the sub and dub. What I am talking about are things like cutting scenes, editting images, cutting or changing dialogue (subs), etc...

Pretty much strong religious aspects, for instance the one we all know and love "Q vs Cross". Other than that I saw not much animation changes throughout .hack//SIGN.

I heard a rumor once that in the Japanese version,  at the end of the series,when Tsukasa and Subaru meet IRL, instead of just hugging, they kissed but again, I neither believe nor disbelieve it, it's a rumor.

.................................... uhm.

 They don't hug or kiss at the end of either version. It shows their hands almost touching.