I don't know if this was intended to be the third season / Gig in the Stand Alone Complex series. I say this as it could very well have been stretched out into the twenty-six episodes the series runs. However, the one and three-quarter hour film manages to get the point across admirably, while still getting the audience to think of what may be ahead for the human population.
Togusa is now in charge of Section 9 after Major Kusanagi retired two years previous. While on a mission, he and his team stumble upon a lead to an Ultra-Wizard Class Hacker the "Puppet Master". This, in turn, leads them to other conundrums and secrets, including the children that are going missing in the city which nobody knows about. Not only do Section 9 have to investigate and solve these mysteries but they also have to resolve issues within the team, due to the major's retirement.
Even with the complexities of the story and all the twists and turns within it, the screenwriters Shotaro Suga, Yoshiki Sakurai, and Kenji Kamiyama (who also directed) do a great job to tie it all together in a comprehensible and intelligent way.
For me, this is the best of the three story lines in the Stand Alone Complex series as it holds some viewpoints that are relative today. We already have puppet masters in today's society and our elderly population is living longer, it's not too far of a stretch to imagine the film's visions becoming future truth, should we start to wonder down the techno-path. People are already talking about populace explosion... These are issues to fire up the brain cells.
The animation is on par with the series, which is to say, of a high caliber, though still not up to the beauty of the 1995 original, and this can be said for the direction and soundtrack also.
You do not need to watch the Stand Alone Complex series to enjoy this film as it is a stand alone in its own right. I would recommend that you at least watch the original Ghost In The Shell before checking this out, though it's not necessary. You do need to set time aside to watch the movie, any interruptions may affect your overall enjoyment and understanding of the story. It's also a film NOT to watch with people who don't get the concepts of Cyber Punk Science Fiction...