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 is a Japanese cyberpunk media franchise based on the seinen manga series of the same name written and illustrated by Masamune Shirow. The manga, first serialized in 1989 under the subtitle of The Ghost in the Shell, and later published as its own tankōbon volumes by Kodansha, told the story of the fictional counter-cyberterrorist organization Public Security Section 9, led by protagonist Major Motoko Kusanagi, and is set in mid-21st century Japan.
Animation studio Production I.G has produced several anime adaptations of the series. These include the 1995 film of the same name and its sequel, Ghost in the Shell 2: Innocence; the 2002 television series, Ghost in the Shell: Stand Alone Complex, and its 2020 follow-up, Ghost in the Shell: SAC 2045; and the Ghost in the Shell: Arise original video animation (OVA) series. In addition, an American-produced live-action film was released on March 31, 2017.
Definition from Wikipedia – Ghost in the Shell