WARNING: The following contains spoilers for Season 1 of Ghost in the Shell: SAC_2045, now streaming on Netflix.
Picking up from the Stand Alone Complex continuity, Ghost in the Shell: SAC_2045 weaves a mysterious storyline. Here, there's been a collapse in the global economic system, which is some 15 years later known as the Synchronized Global Default, that sees paper and digital currency being rendered null. This has created the Sustainable War between countries, and the shocking emergence of the near invincible post-humans has reunited Sector 9 in Japan.
As the Major's crew begins investigating, they're placed in a tricky spot as the country's Prime Minister, Tate, is an American puppet, although he's fighting back against the regime that installed him. Leaving the politics to Tate, Sector 9 discover a post-human named Takashi, who is the focal point of final few episodes and may hold the key to winning this new world war. However, the cost seems to be more than they bargained for.
TAKASHI'S TRUE PURPOSE
Togusa, Major's right-hand man, has become infected studying data they took from Takashi's home and school. The 14 year-old student created the deadly social justice warrior app, Think Pol, which allows society to hunt down corrupt politicians and public figures. It seems, though, the kid had been infected with a virus in the wake of its launch that turned him into post-human. This appears to be due to unique viruses and malware that affect people's cyberbrains and evolve them into warriors more advanced than Major and Togusa.
Togusa, driven by clues in his infection, takes his comrade, Batou, to visit an old countryside home Takashi spent time in. There, Togusa starts to learn more about Takashi's disappearance. He discovers the ghost haunting Takashi is actually his young cousin, Yuzu, who was tragically killed when they witnessed a hit by corrupt government officials.
Takashi was up in the mountain reading George Orwell's 1984, as he wanted to rebel against society, having been given the book by the Airborne Fighter hiding out in the hills. The lead fighter arrived and tried to save the kids but stray fire caught Yuzu while Takashi hid, and as he grew older, he began creating the Think Pol app, until this apparent post-human infection caused him to go missing. Takashi begins to empathize with the boy, but Batou has no clue what's going on, as he can't see his colleague re-living Yuzu's death.
TOGUSA'S NEW JOURNEY
At the end of Takashi's memories, he begs the Airborne Fighters to take him and Yuzu's body. The rest of the battalion are in the back of the truck, and the leader sees potential in him. This appears to be the training the kid undertook secretly before returning to school, and shockingly as the past and present merge, the older schoolboy version beckons Togusa to join him in the truck. Togusa accepts, and when Batou turns around, his friend is missing. Tachikoma and the other rollers (mobile tanks) somehow see Togusa departing with Takashi's legion but Batou can't, and the season ends with him screaming his friend's name.
This is a very intriguing finale because we don't know why Tachikoma and the rollers can see Togusa's exit, but Batou isn't able to. It could mean Takashi has chosen the A.I. he believes is worth fighting on the post-human side of the war, and apparently, he sees Togusa and the rollers as pure souls. It's evident from when Togusa tried to save Yuzu in the memory bank from being killed. It also suggests Takashi, who appears to be the Chosen One by whoever created post-humans, is taking Togusa to the main hub to meet others like him and possibly, the creator of the virus himself.
There's still a lot to learn about post-humans and the shady overlord, as it seems that person created this species of technologically evolved humans as a response to the Sustainable War. Batou and Major suspected as much, but they're between a rock and a hard place, as America is using Japan to have them capture these post-human prisoners for their own research. Hopefully they can connect with Togusa soon for answers, because from this ending and Takashi's words, Sector 9 has been fighting on the wrong side of this war and is helping create an oppressive new world order.
Ghost in the Shell: SAC_2045 is directed by Kenji Kamiyama and Shinji Aramaki. Season 1 is currently streaming on Netflix.