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Originally Posted by Aidan

Ehh she does give a WTF glance at the generic looking dude from what I could see. She might just not have realized that it was one of her cyber bodies. If what you say is true, he would have had no reason to let her see her face in the end. It would just have been, hey look it's me, got ya.

Spoiler:

I believe that Motoko was fighting herself in the end, Kuze wasn't a master hacker in the first place, stand alone complex.

Spoiler:

WTF is an understated reaction when some strange guy walks out of your supposedly secret hideout, IMO.

He did have some hacking skills among his other talents. Remember how he wrote that program to secretly hack the bank accounts to raise the funds to buy plutonium, and how ran a secured cyberbrain hub that the Major had to jack a refugee to break through? He wasn't a wizard hacker like the Major, but as Batou says, the Kugutsu Mawashi abductions was shoddy and not the work of a master hacker by any means. The Kugutsu Mawashi also admits himself he is no match for the Major.
Also, he is the only person that the Major knows that has the gall _as well_ the uncanny charisma needed to pull something like this off, not to mention he already has experience with such cyberbrain hub conspiracies in 2nd GIG.

The theory also stays true to the theme of Motoko having "married" the Puppetmaster at the end of the original Ghost in the Shell manga and movie.