I highly dislike the idea of this Ghost in the Shell adaption, because it will most likely resemble something akin to the turd that was Spike Lee’s “Oldboy”, or a better financed flop like “Aeon Flux, with most of the soul squeezed out in favor of boilerplate action sequences & lens flares.
However, this is how I would do it. For a spoiler TL;DR, skip the following paragraphs to the end.
The adaption could be a prequel set in the USA on the verge of balkanization, taking ideas from the Stand Alone Complex universe, where the USA eventually splits into a smaller USA, Russo-American Alliance, & the American Empire.
Beginning scene could be a mission Scarlette Johanson’s character in the task force known as Section 7 (or some other name) that involves a raid on a suspected hacker that has been murdering high ranking military officials, & foreshadows the later main adversary of the movie.
Scarlett Johanson is a new character, known in the past colloquially as "The Major” due to her combat background.
She’s enhanced (i.e. cyberbrain, but not a cybernetic body) but not fully cyborg yet, struggling to stop all out war amid a top secret task force given clearance above all other agencies & ranks (Section 7). The issue of whether she is human or not due to her cyberbrain but human body could be raised, & she is already in doubt about her own identity & the rationalizations of keeping a human heart vs. the advantages of being fully cyborg.
The pressure from her superiors to further her cybernetics is an issue brought on by a past incident with an older partner that died because Johanson’s character choked during an operation, leading her down the path of augmentation. Her uncertainty plagues her character’s actions, & is later brought into focus by a new partner.
In the background amid character interactions, news broadcasts could elaborate the status of the near future USA on the eve of political turmoil, polarization, & corruption, & Japan discovering nuclear scrubber technology via micromachines, with the Fukushima incident being the catalyst. Thus, the beginning of a massive economic recovery that becomes known as “The Japanese Miracle”.
She has a reputation for being a lone wolf, despite being forced to pair up with a new partner transfered from Japan, Togusa, whom sympathizes with ScarJo’s reluctance with further cybernetics, but see’s her as a hypocrite for basically being a cyborg already without the physical advantages.
The enemy from the earlier opening scene is a hacker who, in addition to murder, is strategically hijacking military official’s ghosts to place regions in the US against each other, with primary factions beginning to emerge.
Amid the cat & mouse game, Togusa is seen communicating with a certain Chief Arumaki, whose newly established Section 9 unit has sent Togusa to keep an eye on this hacker, who originated in Japan but was chased out of the country into the US. ScarJo overhears one of their conversations, & is suspicious of Togusa being a double-agent, especially when Arumaki admits an interest in her record.
It is here where ScarJo’s character could be revealed to not have any real background of sorts, & was in fact an orphan. This vague background could reinforce ScarJo’s own doubts of her identity, since she does not know her parents, her last name, etc. She was adopted by a military official, the very same official that is her boss in the task force & the military is all she knows.
The Hacker gains access to their HQ by hijacking the head of the task force’s ghost, & imprisons Togusa. He then briefs the rest of the task force of a new operation: an ambush within a region of rebels trying to succeed from the United States Government, under the guise that the hacker is one of the rebels.
ScarJo’s boss is compromised from the hacker, and he informs her that Togusa is a traitor. ScarJo reluctantly agrees, having her own doubts on Togusa. But she begins to see that this person is not the same man that raised her as her father. This is further reinforced by the her being cut-off from preparation of the operation, as her father forms a new hand picked unit of lesser known operatives, dubbed Section 8.
ScarJo later covertly visits Togusa with her signature stealth camo, who admits that if he tells her anything more, his cover will be compromised, but that there is far more at stake here than a simple secession movement. He sets up a meeting with Arumaki and & a hesitant ScarJo for later that night.
Arumaki informs ScarJo of the situation, and it is here that we learn that the Hacker behind it all, The Conductor, is a primary instigator of the USA being destabilized. The hacker is revealed to be an ex-member of Section 6, Dr. Kairaishi, who was lead of something called Project 2501, whose aim was to create an advanced Artifical Intelligence.
He fled the project after being labelled a fraud by his superiors, as they believed the A.I. to be far too erratic to be useful: it worked far too well in some instances, & horribly in others, leading to the belief that his work was possibly intentionally fraudulent, as he was found shopping his designs to other agencies.
He went underground for a while, but re-emerged as a robber known as The Conductor, who became notorious for being the first to extensively using ghost hacking in a string of robberies Arumaki believes were to fund his operations abroad in the USA.
He sent Togusa, whom does not have any cybernetics so is immune ghost hacking, to Section 7 in the US, as they began to hear reports of similar ghost hacking in the military, with similar M.O.’s, but on a far more advanced level than simple optical trickery or mis-direction.
The Conductor was becoming skilled enough to hijack entire cyberbrains, & was utilizing this power to destabilize countries for unknown ends, possibly monetary or ideological. Arumaki knew from his contacts in the USA government that the nation was not prepared for such encompassing cyberhacking, with decade old infrastructure in some cases, let alone the new threat of ghost hacking.
ScarJo is further overwhelmed when Arumaki confirms that her father has been compromised by the hacker, & that she is possibly the only one close enough to him that can stop him. She agrees to help, but dreads the thought of killing the only family she knows.
Togusa is freed by ScarJo, & the two head out to the location of the succession movement before the task force arrives. ScarJo uses her stealth for surveillance, & discovers that her father has planted some of the new Section 8 undercover as rebels to incite a riot.
The task force arrives, & it plays out horribly when a Molotov is thrown at Section 7, beginning a bloody shoot-out. ScarJo amid the chaos sees her father retreat to a cave nearby & finds him arming a nuclear weapon of sorts inside of the expansive underground munitions facility.
She confronts & outs him as the Conductor, which makes her father drop the ruse & begin shooting at her. She holds her own, trying to argue past the hacker, but he has total control of his cyberbrain. The Conductor mentions amid the fighting that his aim is ultimately patriotic; that he & his backers will bring down the dominance of the USA & with their advanced A.I. tech, make Japan the new dominant global player.
ScarJo counters than he’s selfish & power hungry, with the Conductor not denying either accusations. He even mentions that he is on the verge of going beyond a physical body or a cyberbrain, & and that when he does, quote: “The world will be all a stage. I will be the one pulling the strings.”
ScarJo, losing the physical battle despite Togusa backing her up, asks her partner about the first case he worked on that involved him. Togusa mentions that there was only one witness who remembered him: a younger boy with a cyberbrain that tried to counter hack the Conductor, which left the only lead that allowed Section 9 to trace him back to America.
ScarJo, who has been seen using her own hacking abilities throughout the movie, decides on a last ditch effort since the time is ticking to disarm the bomb.
ScarJo, with Togusa acting as a distraction, attempts to hack the Conductor, & is initially successful, but he is too skilled for her, and she is ultimately hijacked herself, leading to a scene where she gets a true glimpse at his character.
Togusa is injured by Hacked ScarJo, but is able to make his way to the bomb when ScarJo struggled to resist the Conductor long enough. The Conductor whispers in her mind that she is not strong enough, & mentions that even if he dies, that will not be the end of him.
ScarJo screams to Togusa, who can’t figure out how to disarm the bomb, to get the hell out of there. She decides that he’s already taken everything from her, & flashbacks to her and her father’s life together occur in her mind.
ScarJo decides that she’ll take down the Conductor and herself with the bomb, knowing full well the incident of the rebels & Section 7 being killed would ignite a possible war. Grabbing it, she high tails it out of the underground facility, & away from the rebels base. Just as The Conductor wins back control of her body, the bomb goes off & ScarJo is close enough by the blast to be nearly killed off, & the screen fades to black.
The epilogue of the movie shows a human female body in the hospital awakening from sleep. Reaching over for a hand mirror, she is surprised by what she sees: a different face. She has purple hair, lighter purple eyes & and a more lean muscular body. She is joined by Togusa & Arumaki, & is called by ScarJo’s character’s name.
Togusa explains that he was able to find cover from the blast & called for Arumaki for emergency transport to the nearest Section 7 underground facility for treatment. The female is surprised & somewhat confused, & notices her reflection. ScarJo is now in a completely different body; a fully cybernetic body.
Arumaki mentions that while it was highly risky for a human body so close to death, the surgery was successful due to the latest female model they choose: Model 705A-K0006, or MOTOKO, for short.
ScarJo, struggling to get out of bed & adapting to the weirdness of no longer being in her own body, & her voice sounding somewhat different, asks the two what happened to The Conductor.
Arumaki, with a more stern face, mentions that his ghost wasn’t recovered from her body, nor from the body he originally was using miles away in the vicinity. ScarJo looks off & mentions that he had said something about going “beyond either human or cyborg…” & all three are troubled by this prospect. Arumaki decides to keep the case open upon ScarJo’s request.
The end of the movie ends with ScarJo arriving at Arumaki’s office in Section 9, and being asked to join, since now her old task force has been dismantled due to investigation. Legally, ScarJo is now dead, & Arumaki mentions that she’ll have to choose a new name before her paperwork is advanced through the system, & join Section 9.
ScarJo looks to Togusa, who shrugs, & then looks down at her wrist, turning it right side up to see the same model number: Model 705A-K0006.
Scarlett Johanson: … my name is Motoko.
Cut to black. End credits.
**TL;DR:**
The entire movie adaption is a prequel that fleshes out a possible background for Motoko Kusanagi, originally an American (Scarlett Johanson’s character) recruited by the Japanese government out of the fallout of pursuing a cyber criminal terrorist known as The Conductor. After the final confrontation, Scarlett Johanson’s character is only able to survive by being implanted into a top of the line, custom Japanese cybernetic female body, due to the extensive damage of her original organic body. She takes her first name from the shorthand label for model number of her cybernetic body, & becomes Motoko Kusanagi.
The Conductor was one of the first widely known criminals to use ghost hacking first in Japan, then abroad in the USA. The Conductor’s actions caused the USA to further meltdown into balkanization, & is a warning for nations world wide about the extensive problems of world wide adoptions of cybernetics amid society as a whole.
This presumably means that nations across the world also erect similar task forces to that of Section 9 to combat the new era of crime & political intrigue.
The Conductor (real name: Dr. Kairaishi) was originally project leader for Project 2501. In the end, it’s hinted that the Conductor’s ghost survived & eventually went on to become and/or create…The Puppet Master.
Note: I edited this a bit based on earlier feedback from this reddit thread. Regardless, it was obvious I threw this together over more than a few cups of coffee this morning, haha.