This main storyline was removed from the current movie in cinemas and only exists in a sadly butchered manner.
I watched the anime and must say I favor the tonality and tranquility in the scenes and sounddesign used in the anime. The current movie in cinemas puts to much effort into close ups and action. A little more grandios Blade Runner mood would have benefited the remake. Specially given that the anime was a great source. Also this scene explains much more about the Puppetmaster (a term not used in the cinema version) then the whole 2016/2017 remake has to offer.
Also make sure to watch the original connection between the Puppetmaster and Kusanagi and their dialog about the intentions and goals driving the Puppetmaster.
Update: There is a scene in the recent movie version in which the Puppetmaster controls a hacked body but the dialog falls very short on explaining essentials and stays mainly obscure about origin details. The recent movie also falls short on the topics of A.I. and emergent consciousness. It rather attributes the origin of the Puppetmaster to the same project Kusanagi has been manufactured from …
Ghost in the Shell
Ghost in the Shell (Japanese: 攻殻機動隊, Hepburn: Kōkaku Kidōtai, "Mobile Armored Riot Police") is a Japanese media franchise originally published as a seinen manga series of the same name written and illustrated by Masamune Shirow.
Definition from Wikipedia – Ghost in the Shell