List of Ghost in the Shell: SAC 2045 episodes

The Major meets up with Batou, Saito, Ishikawa, and new recruit Standard (who Batou nicknames "Clown") on the war-torn roads of Palm Springs as they try to find the person supplying local bandits with high-powered weapons. Meanwhile, a newly-divorced Togusa has returned to police work in Japan when Aramaki calls for his help with a new investigation. Back in Palm Springs, the Major's group meets up with a confidential informant who claims that the belligerents are getting weapons from a "Good 1%er" but doesn't know who that is, when they suddenly walk into a robotic guard dog.

The belligerents in Palm Springs take heavy losses but shoot their way through the Major's group using a high-tech APC and drone with Hellfire missiles. The Major manages to down the drone while her team disables the APC, but the supposedly downed drone fires a missile at a mansion in the distance, destroying it. Meanwhile, in Japan, Aramaki tells Togusa of the new Prime Minister's plan to revive Section 9.

The Major's GHOST squad is apprehended by a US Delta Force cyborg squad. An American agent calling himself John Smith hires GHOST for a rescue mission, and has them perform a variety of VR training exercises, while secretly planning to have them killed afterwards. Meanwhile, Togusa tries to contact the old Section members, and he follows the trail to California, eventually meeting with one of the Major's Tachikoma.

Togusa accidentally helps John Smith confirm GHOST's identities while being warned not to dig any further. The Major's Tachikoma ask Togusa to help repair their damaged comrade. Aramaki finds out the NSA is using GHOST, but can't recover them through his contacts, forcing him to ask the Prime Minister to intervene. GHOST is dropped into action near Beverly Hills, where they realize their target is a robotics entrepreneur named Patrick Huge, and that the mission is not a rescue but an abduction.

The Major's GHOST squad infiltrates the home of Patrick Huge but is unable to apprehend him, as he inexplicably dodges all their gunfire and most of their attacks. After fighting through Huge's security robots, the team fights Huge himself, equipped with an armored suit. The team manages to disable the suit and the Major tries to dive into Huge's cyberbrain, then orders Saito to shoot Huge in the head before she loses herself. As John Smith and Delta Force operatives plan to kill everyone there, John is ordered to stand down by the President as Aramaki appears to escort Section 9 back home.

John Smith confirms that Patrick Huge was the "Good 1%er" supplying the bandits with weapons, then escorts the GHOST squad to a secret government facility where he is holding Gary Harts, a retired US Army Master Sergeant and the first known "Posthuman" who almost single-handedly launched a nuclear missile at Moscow until he was rendered inert by a lucky shot to the head. However, the supposedly brain-dead Gary uses coded messages to perform a buffer overflow attack on the facility's emergency systems, taking control of the security robots. The Major orders Batou to kill Gary before he can escape his confinement.

Batou heads to a bank in Fukuoka to deposit his earnings from his work with GHOST, but suddenly finds himself embroiled in a bank robbery concocted by a few senior citizens who lost their retirement funds in the Simultaneous Global Default. After listening to their stories, Batou decides to help them by depositing his funds at the bank, then using his account to short-sell a cryptocurrency using the branch manager's terminal before the SAT storm the building to rescue them. The seniors split their funds, the branch manager gets arrested for the cryptocurrency's crash, and Batou reunites with Section 9.

Section 9 meets with Japanese PM Tate and John Smith, who informs the group there are 14 known Posthumans around the globe (including the two killed earlier) and three of them are in Japan, but there is no footage of them after they transformed. Aramaki offers to let each member decide if they want to work with Section 9 on this new case. The Major tasks Togusa with rooting out the mole in Tate's office. After Togusa roots out the identity of the group spying on Tate, Section 9 gets their requested budget and collectively decides to take on the Posthuman case.

Sanji Yaguchi, a boxer turned Posthuman, is spotted in Fukuoka killing a bureaucrat with his fist alone. Purin compiles data suggesting that Sanji has been serially murdering immigrants and refugees linked to Tokyo reconstruction projects. Tate's father-in-law, who runs the company profiting from the reconstruction, is soon killed in a similar manner. Tate decides to lure Sanji out by making himself the bait. The Major and Batou work together to take down Sanji. The Major wonders why Sanji didn't immediately attack Tate, as John Smith takes Sanji into his custody.

Purin is on the case of a mid-manager who died at an airport when 3 million hackers were somehow directed to attack his cyberbrain at the same time. She tracks down a suspect named Koji, who leads her to a master hacker called the "Nameless King." The King tells Purin about their program "Think Pol," used to enact mob justice on a chosen target remotely, when the Major finds out the King is a highschool student named Uotori. Uotori tells the Major that someone else from his middle school wrote the original program, but he spun off Think Pol to "democratize" it. Suddenly, the program chooses Tate as its next target, forcing Section 9 to spring into action and save him.

The Major and Togusa begin investigating the original Think Pol developer, a Posthuman boy named Takashi Shimamura, and visit his old home to interview his mother. In the past, Takashi developed Think Pol and successfully used it to kill a teacher suspected of abusing a female classmate and leading to her death. After the Major and Togusa leave, Takashi's mother finds Takashi somehow left his favorite blanket on the desk with a letter to her.

While analyzing code written by Takashi, Togusa stumbles over a program meant to awaken forgotten memories. Togusa and Batou decide to follow their last lead to an old, abandoned village in Kyoto, where Takashi briefly stayed with his uncle. Upon arriving in the village, Togusa begins seeing some of Takashi's older memories: meeting a JSDF Ranger, reading a translated copy of George Orwell's 1984, and witnessing a gunfight where a stray bullet took the life of his cousin Yuzu. At the end, the memory of Takashi offers Togusa a spot on a truck. Batou suddenly loses sight of Togusa as the Tachikomas wave goodbye to him.

Section 9 hears of a Russian cyberbrain engineer named Kukushkin claiming to have knowledge about the Posthumans' code while seeking asylum in India. Kukushkin is poisoned with polonium by a Russian assassin before the group can save him, but the autopsy shows the corpse was a robotic body double. The Major tasks Batou and Purin with finding the real Kukushkin. As the two search his room, Purin deduces that Kukushkin transferred his consciousness into an assistant bot, but is unaware of a Posthuman woman named Suzuka Mizukane looking over her shoulder. The Major hunts down Suzuka before she can leave with Kukushkin but loses her in the crowd. As the Major, Purin, Batou, and Paz leave with Kukushkin, they are attacked by the Russian assassin, and after defeating him, notice Suzuka speeding towards them armed with heavy weaponry.

Section 9 fights off both Suzuka and a couple of American special combat cyborgs on the bridge as they attempt to capture Kukushkin for their own reasons. Purin uses a trio of Tachikomas to chase down Suzuka but is forced to stop her pursuit when Suzuka wirelessly hijacks a passenger jet and aims it right at Purin, forcing her to hack into the jet herself and steer it away. As Section 9 carries Kukushkin away, Aramaki meets with Tate to discuss a traitor in his office who leaked information about Kukushkin to John Smith.

The Major tasks Purin with talking to the AI in Kukushkin's cyberbrain. Purin connects with it and discovers the AI named 1A84, developed by the NSA to find a way to make all of humanity prosper while giving the American Empire an extra advantage. 1A84 tried to satisfy their command, and decided that war would be the quickest way to make humanity prosper in the long run. However, its actions ended up creating the Simultaneous Global Default that plunged the world's economy into chaos and made most of humanity worse off. The NSA soon threatened to put 1A84 into stasis when it wouldn't give them their desired answer, so 1A84 implanted itself within the brains of various humans, both to escape the NSA and to try to understand human emotion while completing its overall objective. 1A84 then tries to install itself into Purin's cyberbrain, but soon remarks that it was already "used" by another. Meanwhile, Saito and the Major finish tracking the mole in PM Tate's office, and discover it is John Smith himself. As the Major and Batou arrest John Smith and escort him out of the PM's office, the Major is alerted to Purin sneaking out of Section 9 and stealing a car, heading for the PM's office herself. As Purin approaches the PM with a pistol, she shoots one of Tate's SP's before he can assassinate him, but is gunned down by the rest of his escort in response.

After John Smith is locked in a cryogenic chamber, Tate and the Japanese government meet to decide the fate of Section and Purin. Meanwhile, the Tachikomas decide to do their own investigation into Purin's past, in hopes of saving Section from disbanding again. After traveling across Niihama, the Tachikomas find an external storage cluster. As they read the stored memories, they find that Purin, as child, was involved with one of Section 9's cases from fifteen years ago when her entire family was killed by Marco Amoretti. She was rescued by Batou and put into witness protection shortly thereafter. Unbeknownst to the Tachikomas, Sections 9 have been tracking their progress resulting in Batou becoming distraught over not recognizing Purin sooner. Eventually, Section 9 and Purin are cleared of suspicion, with the blame for the assassination attempt placed on the SP that Purin shot. The Tachikomas decide to use Purin's stored memories to create a new prosthetic version of her, while one of them inserts the 1A84 code into her program.

Togusa is reliving his memories of working as an undercover police operative. After resisting torture and chatting with another man named Noda, the gangsters demand Togusa shoot Noda to prove his loyalty, but Togusa refused and escaped with Noda into a snowy wilderness, only for Noda to sell him out. As his enemies surround him, Togusa questions his own memories, when suddenly he wakes up on a train with Noda. The train arrives at "N." As everyone steps onto the platform, Noda reveals that Togusa's flashback was actually his own, and he carried the guilt of selling out his partner until "Big Brother" used "Miniluv" to purify his heart. Togusa tries to find Takashi in the crowd by the platform but loses him. Unable to reconnect with his team wirelessly, Togusa stumbles upon an old, abandoned tobacco shop with a pay phone, and calls Batou via landline.

A 3D-printed copy of Suzuka infiltrates the USS Arkansas and massacres the sailors on board. Back in Niihama, Section 9 traces Togusa's call to a phone near "Shin-Tokyo Station." Batou, Ishikawa, and Saito head out to retrieve him, while the Major warns that about three million people have gathered in the same area for some unknown purpose. Meanwhile, Togusa wanders into a supposedly unfinished construction site, only to find a bustling street market with a wide variety of people gathered around. Togusa's ignorance of the situation causes the crowd to label him "N-Po," and a schoolgirl named Kanami escapes with him, warning that he'll be sent to "Room 101" if he's captured. Later, Tate tells the Major and Aramaki about the Arkansas hijacking, and the message that the Posthumans now have a nuclear submarine to wage war as the Nation of N. Togusa continues trying to evade his pursuers while following a surprisingly agile Kanami, when he's saved at the last minute by Batou. The next morning, American special forces begin airdropping into the area as Saito discovers Takashi and Suzuka standing near their landing zone.

Section 9 and American Special Forces both race to deal with Suzuka before the threat of a nuclear strike becomes realized. Tate decides to call in the JSDF to stop N before they spark a civil war in Japan. Purin wakes up and realizes she has a new, fully-prosthetic body after dying from Tate's bodyguards, and decides to hitchhike her way to Tokyo to rejoin Batou and the Major. The Americans find Suzuka, but all of them have their cyberbrains hacked and shoot at each other. Batou and Togusa track down the one survivor of the American unit only to find out the man is Standard. Purin finds out the driver of the van she hitched a ride on has accepted "Big Brother's" message, a copy of the Miniluv app that Takashi indirectly used on Togusa, and is driving her to N. The van with Purin and the driver is stopped by a JSDF blockade on a bridge, but on the other side of the blockade a lone Takashi walks towards the JSDF.

The JSDF soldiers begin crying and clear a path for the van as Takashi disappears and Purin wonders how he could hack them in Autistic Mode. Purin kicks the young man out of his own van, who then gets arrested by the Thought Police. Standard tells Batou and Togusa that the Posthumans supposedly have a 15-minute hibernation window, and were trying to confirm it so they could hold them hostage, as if either Takashi or Suzuka died, the other would launch the nuclear missiles from the Arkansas. Purin tries to locate Takashi through the internal N network, while Togusa spots her, and Standard sends out a laser signal. Ishikawa's helicopter is shot down by hacked JSDF troops, but manages to escape the wreckage in a Tachikoma as The Major decides to shift her plan to arresting Takashi and Batou's group decide to arrest Suzuka while they have a chance. Batou is nearly shot by Suzuka who appears as The Major when the real Major chases her off. The Major deduces that the Posthumans used digital tags hidden in wall graffiti to infiltrate everyone's cyberbrain even in Autistic Mode. Purin finally locates Takashi.