On their fifth wedding anniversary, Amy goes missing and Nick finds himself suspected of her murder. It wouldn't be fair to reveal what happens next. Suffice to say, Amy and Nick make extremely unreliable narrators. Flynn's novel is gripping and horrifyingly astute on the subject of relationships, and often laugh-out-loud funny.
"Every marriage involves gamesmanship, little power-plays and squabbles and pettiness," says Flynn. "I just amplified that - a lot."
Fifty Shades aside, Gone Girl was the other US publishing phenomenon in 2012. Flynn - whose first name is pronounced with a hard "G" - had previously written two reasonably successful novels, at nights and weekends, while spending her days as a TV and film writer for Entertainment Weekly magazine. But then, just like her characters, she was laid off.
The 42-year-old admits her own experience crept on to the page.
Born in Kansas City, Missouri, Flynn moved to New York as a journalism student and, like Nick, she was "a kid with a chip on [her] shoulder about being from the middle of the country and not having been to an Ivy League school, who is dropped into this rarefied environment".
In one of the book's more autobiographical passages, Nick describes arriving in the city during the late 1990s: "The last gasp of the glory days, although no one knew it then.
New York was packed with writers, real writers, because there were magazines, real magazines, loads of them. This was back when the internet was still some exotic pet kept in the corner of the publishing world ... a time when newly graduated college kids could come to New York and get paid to write. We had no clue that we were embarking on careers that would vanish within a decade."
Flynn worked at Entertainment Weekly for 10 years before falling victim to a round of redundancies in 2008.
"People told me it was great that I'd lost my job because I could be a novelist," she says, "but I loved my job so much. I never got over that thrill of leaving the office in the middle of the day to go to a movie screening that I was being paid to write about and talk about to all my dorky film friends."
She already had a few unfinished novels in her desk drawer when she completed her first thriller, Sharp Objects.
"I'd started various books over the years and never got far," she says. "My problem was that I'd be interested in a certain character, but they wouldn't do anything. They'd just hang around in rooms, talking a lot. I remember reading Dennis Lehane's Mystic River through the night without putting it down, and thinking, 'that's what I need to do'. I realised that if I tied a character to a thriller-plot device, it would give me the discipline to keep moving the story forward."
Her debut was published in 2006, and won acclaim from critics and fellow writers, including Stephen King and Harlan Coben. Its central character was a troubled reporter dispatched to her hometown to investigate the murder of two young girls. Flynn followed it up with 2009's Dark Places, about a woman re-examining her family's murder in a supposed Satanic ritual. Charlize Theron is now set to star in a Hollywood adaptation.
Contrary to the impression her books might give, Flynn had a happy childhood, and suggests that her dark imagination developed as a reaction to her safe surroundings.
"I was always fascinated with stories of mayhem and murder," she recalls. Luckily for her, Flynn's father was a film professor. "I have distinct memories of being 9 or 10 and him loading Psycho into our old top-loading VCR machine.
"I loved horror movies. Back when they had local broadcasting we had a 'Friday Fright Night' on television every week, which I'd be allowed to stay up for."
Unlike so many other genre novels, Gone Girl has memorable passages not only of action but also of reflection. In one such extract, Amy reflects on the myth of the so-called "Cool Girl". Being a Cool Girl, she thinks, "means I am a hot, brilliant, funny woman who adores football, poker, dirty jokes and burping, who plays video games, drinks cheap beer, loves threesomes and anal sex ... Men actually think this girl exists.
Maybe they're fooled because so many women are willing to pretend to be this girl."
Flynn admits to having once "invested way too much energy" in trying to be a 'Cool Girl' herself. "We often go into relationships playing an emotional con game with each other," she says, explaining one of Gone Girl's central themes.
"You present your best self because you want the other person to like you, but there's no getting around the fact that you're tricking them, because you're not presenting entirely who you are.
"Hopefully, once you figure out a person's darker side and what makes them tick, you understand it and it makes them more interesting. But I liked the idea that you could drill down even deeper and hit crazy."
By sheer coincidence, Flynn and her lawyer husband, Brett Nolan, recently celebrated their five-year anniversary. They have a 2-year-old son called Flynn. Nolan's name appears in each of his wife's books, and in Gone Girl he crops up as an anagram, in Tanner Bolt, Nick's slick, spray-tanned celebrity attorney. He's not the least bit concerned by the comparison, Flynn says.
"My husband has never been threatened by the weird stuff that comes out of my brain. This book obviously deals with marriage, but he said, 'don't censor yourself, write what you need to write and we'll deal with it later if anything's too close to home'."
In the end, apparently, Nolan demanded almost no changes to the text, though he did object to Nick making a reference to gingham. "He thought a man like Nick wouldn't know what that was."
The couple live in Ukrainian Village, a Chicago neighbourhood once populated by Eastern European immigrants who left behind a handful of magnificent churches to be admired by its new inhabitants - "writers, artists, hipsters and yuppies".
Flynn writes in the "mother-in-law apartment" in the basement of their home.
"It's halfway below ground so there's very little stimuli, much less light. In wintertime the old floor oozes cold, so I hunch over my space heater like Bob Cratchit, typing. I could never work in a coffee house. I have to be in my dark little room."
• Gone Girl (Phoenix $27.99) is out now
