Alright quick rundown, may not be 100% accurate
"the nets" stands for the interwebs, and they use the term "neuronet" to refer to the big psychic thingie.
The girl we see talk to Batou isn't Motoko, it's a remote-controlled body piloted by Ishikawa.
The plot is roughly as follows: S9 finds a dead Motoko body, they investigate the anti-prosthetics shinto sect she was trying to infiltrate, Tsunagi tags along with them cause the Channeling Agency told her to, shenanigans happen.
They get attacked by goons probably sent by a chick who's trying to run for mayor and really likes prosthetics (Bouma and Paz are tasked with guarding her and they don't like her) and the goons get attacked by a huge albino guy.
The boss of the sect is bros with the albino guy, and both of them turn out to be bioroids made by a super-secret revolutionary organization called Yomotsu that did stuff during the war. They got the torso of a broad in a tank, dunno what that's about.
Motoko/2501 contacts Tsunagi with her psychic powers, tells her in needlessly cryptic terms to go find a secret base in the ocean. She and Togusa go there, she remembers everything, turns out that she's one of the bioroids made by Yomotsu but then the Channeling Agency grabbed her and erased her memories, and the boss of the Channeling Agency tells Aramaki about it.
But then they get attacked and Togusa gets fucking shot in the head.
Batou and Ishikawa are in kansai, they get into a slapfight with the yakuza, then find out about an underwater base possibly sponsored by the mayor broad, not sure, and sneak in.
And that's about it for now.
