Why wasn't Major Motoko Kusanagi's original shell repaired?

Question

Ghost In The Shell 1995 spoilers ahead

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In one of the final scenes of "Ghost In The Shell" (1995) Major Motoko Kusanagi's shell is destroyed by section 6 snipers.

Right before this happens Batou sacrifices his arm to protect The Major's head. When The Major wakes up she is in a different shell, one of a child. (a black-market shell)

Batou mentions that Section 9 showed up and cleaned everything up. Including the 2 cybernetic bodies and his arm.

Why didn't section 9 repair The Major's shell if they repaired Batou's arm?

I'm not sure what section 9 backup did when they arrived and found The Major's head. Why are they in a safe house instead of at section 9 headquarters? The way I see it there are a couple explanations, although I feel like these aren't the best, as they each leave out a thing or two:

• The Major is still an expendable asset, and they can just buy another cyborg from a company. Or rebuild The Major back in section 9.
• The Major was actually repaired and is in section 9. The Major we see at the end of the movie is considered separate due to the Puppet Master merge. Batou saved this forked version of The Major and hid her away. There are now 2 versions of The Major.

Is there anything I missed in the movie to explain this point?

I just started watching all the "Ghost In The Shell" movies & series. I would appreciate it if the conversation was scoped just to the original 1995 movie to avoid spoilers

Answer 1

Section 6 was attempting to cover their tracks with respect to the Puppet Master. Since Motoko and the Puppet Master had merged, we must assume that they would want to destroy the post-merge Motoko as a loose end. In fact, they would have succeeded in this goal had Batou not deflected the bullet intended for Motoko's head. After the snipers fled the scene, Batou hid her head, leaving only the body to be cleaned up and allowing the presumption of her death.

Section 9 can rebuild the Major's shell, but her brain is unique. There are not two versions of the Major. Batou transferred her head to a black market body to allow her to escape, and a child's shell was the best he could do in short time. Hiding her head, giving her a new body, and taking her to a safe house allowed her to escape from being pursued as the new iteration of the Puppet Master (and allows her to escape the life she was already questioning throughout the movie).

The Ghost in the Shell wiki could provide further clarification of these characters' motives.