Henry Dorsett Case is having a rough day. Once upon a time, he was a talented console cowboy (computer hacker). Then he got caught with his hand in the proverbial cookie jar, and his employers made it so he'd never be able to hack a computer again. Now, he's a hustler in Chiba City, Japan where he owes money to a local drug lord. To make matters worse, his girlfriend has just stolen a bunch of RAM he'd planned to fence on the black market.
So when a mysterious man named Armitage offers him a job as a console cowboy on retainer and a chance to hack again, Case decides that's pretty peachy compared to the alternative. He teams up with a street samurai named Molly Millions, with whom he strikes up a relationship. Problem is Molly doesn't trust Armitage, and she has Case dig up any information he can on the guy.
At the same time, Armitage assigns them their first job: steal a ROM construct housing the personality and memories of the Dixie Flatline, a legendary hacker and Case's old teacher. They team up with a group of cyberterrorists called the Modern Panthers, start a teeny-tiny riot, and Molly sneaks into Sense/Net to nab the ROM while Case hacks the system.
With the Dixie Flatline's skills available to him (thanks to the ROM construct), Case hacks into a London database containing Armitage's past. Turns out, the guy isn't Armitage at all but one Colonel Willis Corto. He's only surviving solider from a botched military operation called Screaming Fist. The experience and subsequent betrayal by the American government traumatized Corto to the point of insanity, and psychologists created an entirely new personality to fix the broken one. That shiny new personality was named Armitage. Yep, this some seriously shady stuff.
Crazy as that sounds, Case has no time to do anything with the information. Instead, he and the team are off to Istanbul to pick up another member so they can complete more nefarious missions at Armitage's request. The man's name is Riviera, and he's a sociopath with the ability to create holographic illusions and a drug lust. Gee, wonder if that'll work out for them. Then Case and Co. head to a space colony called Zion where they pick up two Rastafarian pilots, Maelcum and Aerol.
With the entire team now assembled, they head to the space resort Freeside. En route, Case meets a super-advanced artificial intelligence named Wintermute in the matrix. Wintermute is the one pulling Armitage's strings, and the one in charge of the entire operation.
Things go according to plan… at first. Riviera is invited by 3Jane Tessier-Ashpool to come to her home, the Villa Straylight. Meanwhile, Molly follows and infiltrates Straylight secretly. Case has a small run in with the Turing Police, an elite bunch of cops who monitor computer crimes, but Wintermute saves him, and Case sets his hacking program to work on Straylight's defense systems.
Then things start to go straight south and fast. Armitage's personality breaks down, and Corto is released. The broken personality tries to sabotage the entire operation believing he's at Screaming Fist again. Then Riviera betrays the group—big surprise, right? Molly accidently runs into John Ashpool and is forced to kill him before being captured by Riviera and Hideo, 3Jane's ninja bodyguard. Now it's all up to Case.
Case tries to save Corto from himself, but Wintermute launches the mentality distraught soldier out an air locker instead. Moving on to the next problem, Case and Maelcum break into Straylight to save Molly. On the way, Case hacks into a terminal and is drawn into the world of another AI named Neuromancer. Neuromancer is Wintermute's other half, and Wintermute set up this entire operation so the two can be joined together. There's just one problem: for unexplained reasons, Neuromancer doesn't want this, so he offers Case an ultimatum: instead of completing the operation, Case can live with his dead girlfriend Linda Lee in Neuromancer's world. Case declines and finds his way to the real world with the help of Maelcum's reggae dub music. Yep, as loopy as that sounds, that's exactly what happens.
After returning to reality, Maelcum and Case try to rescue Molly but fail. It's okay though as 3Jane has grown bored with Riviera and sics her ninja bodyguard on him. With Molly's help, Case convinces 3Jane to give him the password needed to merge Wintermute and Neuromancer. With only seconds to spare, Case succeeds.
In the end, Molly leaves Case so as not to grow soft. Case meets the merged Wintermute/Neuromancer to learn that the program has now grown to encompass the entire matrix. Case isn't sure what that means, but he does discover that Linda Lee and some version of himself also exist in cyberspace, perhaps within the new AI. The novel ends with Case not knowing what the future has in store.
Whew, did you get all that? Then take a breather; you've earned it.