A prolonged nervous hush has settled on the audience at the Yvonne Arnaud theatre in Guildford. It is broken only by scattered yelps of anxious laughter and the sound of Stewart Lee quietly, inexorably pushing the boundaries of what is comedically acceptable.

He is halfway though a typically discursive and increasingly extreme routine about the Top Gear presenter, Richard “The Hamster” Hammond, who, as it happens, went to the same school as him [Solihull School]. Lee, as the Daily Mail has already noted, “has made no secret of his dislike for Top Gear”. On tonight’s evidence, that is understating the case. Interestingly, it is Hammond in all his cuddly collusiveness, rather than the more obvious Clarkson, that has provoked the comedian’s ire.

“I wish he had been decapitated and that his head had rolled off in front of his wife,” Lee deadpans, referring to that now famous car crash of a few years ago. “And that a jagged piece of metal debris from the car had stuck in his eye and blinded him and then his head had rolled a few more yards into a pool of boiling oil and that it had just retained enough neural capacity for him to be able to think ‘Ooh, this is hot!’ before the whole thing exploded into tiny pieces.”

At the Yvonne Arnaud, most of the audience laugh at this point, the extremeness of Lee’s vision having pushed it into the realm of what might be called the satirically absurd. Others just shake their heads in mystified silence. No one walks out, though, even when Lee turns his comic ire on Guildford, which he suspects is more a Top Gear kind of town than a Stewart Lee kind of town. This, you sense, is just how Stewart Lee likes it. He operates out in that dangerous hinterland between moral provocation and outright offence, often adopting, as in this instance, the tactics of those he targets in order to highlight their hypocrisy.

Lee is essentially a satirist who redefines the term barbed wit; more traditional in his approach than say, Chris Morris, but no less appalled and disgusted at what has become of us.

“The idea of what’s acceptable and what’s shocking, that’s where I investigate,” he says, when I meet him the following week in Soho, London. “I mean, you can’t be on Top Gear, where your only argument is that it’s all just a joke and anyone who takes offence is an example of political correctness gone mad, and then not accept the counterbalance to that. Put simply, if Clarkson can say the prime minister is a one-eyed Scottish idiot,” adds Lee giggling, “then I can say that I hope his children go blind.”

The short bout of Daily Mail-orchestrated outrage that attended Lee’s Top Gear routine is small potatoes compared to the storm of controversy that enveloped him when Jerry Springer: the Opera, the comic musical he co-wrote with Richard Thomas, was broadcast on BBC2 in January 2005. The show had already run for a few years in the West End to great reviews but the screening brought a record 65,000 complaints. The protests were orchestrated by a fundamentalist group called Christian Voice, who were so angered by the portrayal of Jesus that they also brought a private case for blasphemy – later thrown out of court. The same group organised pickets of venues across Britain that showed the musical. “Controversy,” says Lee, sighing, “seems to be a by-product of what I do rather like offence is the by-product of a dog urinating on the pavement. It just happens.”

In this instance, though, it seems to have left its mark. More than once Lee returns to the subject. “If you have been on the verge of becoming a millionaire and that has not happened because of far-right pressure groups,” he says at one point, sounding just like he does when he is getting into his stride on stage, “and your work has been banned and taken apart, and you’ve been threatened with prosecution, and the police have advised people involved with your production to go into hiding, and bed and breakfasts won’t have the cast to stay because they’re blasphemers, and you have to cross a BNP picket line to go to work in Plymouth, you do start to think, well, what can be worse that that?”

I ask him if the experience has impacted on his stand-up act in any way. “It did make me feel there was not much point ever trying to reach a mass audience with anything interesting and provocative. You just run the risk of being misunderstood on a large scale.”

In the flesh, Lee looks exactly like he does on stage, the unruly quiff and downbeat demeanour suggesting an ageing indie-rock star. One of the many inspired moments in his show includes a riff about constantly being mistaken for various embarrassing 80s celebrities – “Oh, look, that Terry Christian hasn’t aged well.” He also compares himself to “a crumpled Morrissey” and, when I broach the similarity today, says: “It’s very odd that we seem to be decaying at exactly the same rate.”

When I offer to buy Lee a drink, he opts for a pot of English breakfast tea. He seems affable enough if a little worn out, which is hardly surprising. In August, he launched his new show, If You Prefer a Milder Comedian, Please Ask for One, with a 30-date Edinburgh residency, and then went straight into a 75-date national tour. He is now preparing for a six-week run at the Leicester Square theatre in London. “I’ve worked out that my audience has doubled since the TV show [his quirkily brilliant series, Stewart Lee’s Comedy Vehicle, which had a six-week run on BBC2 last spring]. I can do these bigger small venues but the nuances and gestures will all be lost if I go much bigger. It’s a dilemma.”

What would he do, I ask, if Richard Hammond turned up on the first night in London and sat in the front row with Clarkson and James May? “Oh, I’d just do it,” he says, sounding excited at the prospect. “Clarkson is a rightwing libertarian so he’d probably be all right with it. I’d happily debate the routine with Hammond and I think he’d get what it’s about, that he’s being used as a symbol of the sort of debased crassness that passes for controversial humour these days.”

Lee, for the first but not the last time today, dissolves into a slightly maniacal cackle, the sound of someone who is, like many stand-up comedians, slightly unhinged. He is anything but. The Top Gear section of his three-act show is an intricate and carefully choreographed argument against the current drift of popular culture towards boorishness and casual cruelty disguised as irony.

“It’s interesting to me that apparently distasteful comments from the right against weak targets tend to draw a lot less media fire than apparently distasteful comments from the left against hard targets. That’s one of the threads that runs through the show and that people hopefully pick up on.”

At 41, Lee is now a veteran of the stand-up circuit, and, after 20 years, a master of his craft. His style is relaxed, his delivery slow and sure-footed, and his routines meticulously plotted. The shocks when they come are like powerful punctuation marks in an extended essay. Sometimes, too, he moves beyond the comic into something altogether more dark and dangerous. On YouTube, you can witness Lee’s long and inspired tightrope walk of a routine which targets the Mail’s reigning loudmouth, Richard Littlejohn, and in particular, his dismissiveness of the prostitutes who were murdered by a serial killer in Ipswich in 2006. It is the single most powerful piece of politically motivated satire I have seen since the great Bill Hicks ruled supreme, and inches inexorably towards a pay-off that, when it comes, is both inspired and devastating. It should be studied at length by comedians who think that staged outrageousness as an end in itself is enough.

“I’m now in the position of having to justify myself against the fearless young men of comedy”, says Lee, referring to fellow comedian Frankie Boyle’s recent assertion that fortysomething comedians are too old to be edgy. “The thing about most of those professionally offensive comedians, though, is that no one is ever actually offended. Everyone understands the parameters and operates within them, the audience and the performer. Whereas, with someone like Jerry Sadowitz, there’s a part in every show of his where a little piece of me dies and I think, I wish I’d never heard that. Now, that’s the most truly offensive comedian you’ll ever see.”

It often seems, when talking to Stewart Lee, that he views the whole world through the prism of stand-up comedy, constantly referencing his heroes, which range from the familiar (Dave Allen) through the doggedly alternative (Sadowitz, Daniel Kitson) to the downright obscure (Ted Chippington). It was the latter’s appearance as support act for his favourite group, the Fall, in the early 80s that made the 16-year-old Lee consider comedy as a serious career. “I was the only person laughing in the room but I honestly thought it was the best thing I had seen in my life up to that point.”

Lee was the first of his family to go to university, studying English at Oxford. He wrote and directed, but did not appear in, the Oxford Revue in 1989. “I wasn’t th e classic comedy type, I wasn’t bullied or extrovert. I was more the ambitious literary one who wanted to write clever little plays.”

His parents, he says, were initially “baffled and disappointed” by his career choice. To this day, they ask him when he is going to get a proper job. “My mum’s main reference point is Tom O’Connor. She came to see me in Worcester and it was kind of sad, really. I could tell that she thought most people were laughing out of pity. She thinks I should be doing cruises by now like Tom – ‘That’s where the money is, Stew.'”

In 1990, Lee won the New Act of the Year award at Hackney Empire and the following year, having teamed up with Richard Herring, began writing for Radio 4’s groundbreaking On the Hour. Throughout the 90s, Lee and Herring wrote and performed together. “We met when we were 19 and the core of the act was two teenagers bickering. It was starting to wear out when we were 30.” Their successful radio show, Fist of Fun, transferred to BBC2 for two series, before the duo parted company in 1998.

“We compromised the show’s integrity for the second series,” says Lee. “We were pressurised to change the set and the titles and the whole atmosphere changed. I didn’t want to do it, but I did, and it set me back years. When I see clips of it on YouTube, I look like a truculent, miserable, lazy man.”

In 2001, Lee published a critically well received novel, The Perfect Fool, and created a surreal show, Pea Green Boat, based on Edward Lear’s poem “The Owl and the Pussycat” which showcased Lee’s verbal ingenuity and gift for pastiche. He is writing another book which will comprise the texts of three stand-up routines complete with notes and sources in the manner, he quips, of “Pound’s annotated version of The Waste Land”.

Lee is married to the comedian and writer Bridget Christie and they have a young son. “It’s much harder to fabricate an across-the-board cynicism about everything for commercial ends when you’re largely happy on a day-to-day basis,” he says, quite seriously. “Having a child and imagining you might have a future means that your cynicism becomes a kind of defeated romanticism. You suddenly find yourself hoping for the best. Plus, you can’t be too cavalier about your disregard for commercial success when the comfort of another person’s life is dependent on it.”

Where, then, will he go after the current show completes its long run? He has one vague, but slowly growing, plan to go right out on a limb by touring his version of Michael McIntyre’s current stand-up show in its entirety. “It would be verbatim, word-for-word, gag by gag like some weird recreation,” he says, cracking up at the very thought. Why on earth would he want to do that? “Oh, just to see if I could inject any paranoia and menace or even personality into it, if I could turn the blandness of it into the thoughts of someone on the very edge of madness.”

Then, as is his wont, he suddenly turns serious and thoughtful again. “It would be nice for the TV show to be recommissioned so I could have a year off the road. Then again, I’ve worked out that the economics of a being an obscure cult figure might just work out better in the long run than the economics of being a discarded television performer. As the comedian John Hegley says, if 5,000 people give you a tenner a year, it’s a living.”

If You Prefer a Milder Comedian, Please Ask for One is at the Leicester Square theatre, London WC1, 7 Dec to 17 Jan