What does Major Kusanagi whisper to Batou at the end of episode 25 of GITS SAC?
She said 「な・あ・に」 (na-a-ni, "What").

In Japan, there's a TV program on BS2 channel called BSアニメ夜話 (BS Anime Night Talks), and on 26 February 2009, it's talking about Ghost in the Shell: Stand Alone Complex.

Regarding that scene, the original storyboard revealed that she was supposed to say "na-a-ni". With cold expression, Major Kusanagi didn't convey anything to Batou even in that situation. Toshio Okada (anime producer &amp; co-founder and former president of Gainax) responded with「ドSねーちゃんですね」("She is a very sadistic girl, eh.")



Fun fact: before this information was revealed, many Japanese fans theorized that she was actually saying 「と・け・い」 (to-ke-i, "(Wrist)watch") because


   she tried to tell Batou that she wasn't wearing a watch, which means that she was not the real Major Kusanagi, only a body double of her.


The fan theory was also strengthened by the close-up of her wrist after that scene (spoiler image below)


   




Source:


jademetal's blog post (Japanese)
Yahoo! Chiebukuro (Japanese)