The show's pilot was decidedly darker, revolving around Bernard's, and later Manny's, decision to commit suicide. It featured Manny (surname Zimmerman in reference to Bob Dylan) as a professional depression-o-gram, and the Fran character as Valerie, a philosophy lecturer.

After his accountant flees from the police, Bernard, the slovenly owner of Black Books, is faced with the prospect of doing his own taxes, resorting to pairing his socks, getting drunk with door-to-door evangelists, and trying to seriously injure himself to avoid it. Manny, a high-strung accountant, enters Black Books to buy The Little Book of Calm on his way to work and later swallows it; it disappears before his operation, his baffled doctor musing that it may have been assimilated into Manny's system. Bernard's only friend, Fran, who owns the knick-knack shop "Nifty Gifty" next door, is distracted from being on-call as a friend's birth coach by a sphere of unknown function. Bernard is knocked unconscious by skinheads, and Manny offers to do his taxes.

Bernard wakes up after a night of drinking to discover he has accidentally given Manny a job at the bookshop, and spends the day trying to get rid of him. Manny proves to be a charming, sociable and competent employee. An offering of wine from Manny and the threat of physical violence from Fran persuade Bernard to keep Manny on board.

When the squalor of the bookshop overwhelms him, Manny calls a creepy cleaner, and Bernard reluctantly agrees to house-sit for a friend. Unfortunately, the two manage to drink a very expensive bottle of wine that was due to be presented to the Pope, and have to figure out a way to replace it. Meanwhile, Fran goes on a date with a man whom she soon realises is closeted. She then dates the cleaner.

After celebrating his birthday fueling an all-night The Sweeney marathon by drinking espresso, Manny thinks he is a 1970s policeman and manages to go from eyeing old men suspiciously in the bookshop to being trapped at the local police station helping a real detective put the 'good cop, bad cop' routine on a local villain. Bernard explains how going to a dinner party led to him falling and breaking his arm. Fran describes the steps from seeing her boyfriend having dinner with another woman (wrongly assuming him to be cheating) to being in hospital with a neck injury. The woman is his sister and he ends his relationship with Fran.

After being burgled, Black Books gets a new alarm and security door fitted, but Manny fails to listen to the unlock code, distracted by a Subbuteo player in the installer's hair. This results in Manny being trapped alone inside with only a bottle of absinthe and dead bees for company and Bernard locked outside with just enough money for popcorn and a cinema ticket. Meanwhile, Fran has taken the phone off the hook to listen to silky-voiced Howell Granger read the shipping forecast on the radio, leaving Bernard to wander the streets of London penniless, cold and wet.

Bernard's constant bullying drives Manny to leave. He is attacked by a bee in a telephone box and finds himself on the streets. He is picked up by a photographer and treated to a glamorous life of expensive clothes, satin sheets and crinkle-cut chips in silver bowls, but returns to the book shop after discovering that the photographer has a beard fetish.

Fran decides to learn the piano and enlists the services of an elderly blind Russian tutor. His harsh methods and her inability to master the instrument quickly lead her to quit. Manny discovers he can play the piano purely on instinct, and against all odds Bernard gets a date with an attractive woman. As a result, Fran and Bernard bribe Manny to hide inside the piano, armed with only spoons, in an attempt to make themselves look good.

A heat wave sweeps London, causing Bernard to seek a "summer girlfriend", Fran to suffer from insomnia, and Manny to panic about his 'Dave's Syndrome', a condition that supposedly triggers at 88°F (31°C). Bernard tries to get Manny as hot as possible. Fran discovers the walls of her flat are literally closing in as her unscrupulous landlord creates another flat from the stolen space. Bernard pretends to be her lawyer in an attempt to rectify the situation but quickly falls for the new lodger, Alice. At the end of this episode, Bernard asks Fran when they will admit they are deeply attracted to each other. Fran will not 'Until at least one of us is dead'. The scene returns to Manny's condition having been triggered with disastrous consequences.

While Fran is in desperate need of a job, Manny gets a call from old friend Gus, a diminutive underworld capo. Gus agrees to get Fran a job working for a man named Nugent in exchange for the bookstore hosting a reading of his nephew Danny's new book. Danny is illiterate, and his ghostwritten autobiography describes the pain he has inflicted on many others in great detail. He threatens Bernard and Manny intil they teach him to read within two days so he will be able to record an audio book.

Fran researches her genealogy and uncovers third cousins from Eastern Europe, but after meeting them, wants them to leave her alone. Meanwhile, Manny and Bernard try to re-invent the shop as a trendy café-bookshop, and then as an upscale restaurant. The shop is overrun by a horde of unseen carnivorous insectoids that Manny and Bernard must make an effort to destroy.

Fran returns from a holiday in Cornwall to find Bernard living amongst mouldy books and dead badgers and Manny working next door at the glossy Goliath Books. Manny is out of place amongst creepy micromanager Evan and his staff, but resists Fran's self-serving attempts to drag him back to Bernard so that she has somewhere to hang out. Bernard's physical condition deteriorates rapidly without Manny's care.

Fran leaves for the weekend to go to her friend Becky's hen party while Bernard and Manny, inspired by their latest children's-book event, decide to write and illustrate a book for children. Bernard's first effort comes to over 1,030 pages, and covers Joseph Stalin, a lens grinder, a broken marriage, and a truth-seeking journalist. Meanwhile, Fran's hen party is a disaster.

Manny's irritating parents unexpectedly come to stay after Bernard deletes Manny's answerphone messages. Bernard is infuriated by their quirks and songs, and it is revealed that Manny's letters home have greatly embellished his actual accomplishments in life.

After a small win on the Grand National, Bernard becomes addicted to gambling, leaving Fran and Manny in a bitter competition to sell as many books as possible. Soon horses are not enough and Bernard joins an illegal poker game against a group of ruthless, successful gamblers, including Dave 'Mouse Ear' Smith. Being hopeless at cards, Bernard (now nicknamed The Gold Mine) loses everything, and Fran and Manny need to hatch a plan to obtain the money before Bernard's debtors seek payment.

Manny organises a book launch party at the shop with charismatic but smug travel writer Jason, and everyone starts falling for him and his stories of far-away adventure. Meanwhile, Bernard's landlord has died and a small cat now owns the building. Driven to destroy the cat's burgeoning real-estate empire, he attempts to persuade an animal-loving pest exterminator to kill it. His attempts fail and cause the exterminator to commit suicide. When Bernard tries to finish the job, Manny is injured.