I meet Brian Wilson in the tiny, windowless conference room of a Mayfair hotel, where he is promoting his latest series of British concerts accompanied by his musical director, Jeffrey Foskett. The former leader of the Beach Boys sits bolt upright, a portly, 69-year-old man with his grey hair arranged in a kind of quiff. There is, as everyone who meets him seems to note, something ineffably sad about his eyes, even when he laughs, which he does in a gruff, mirthless shout. He rattles through questions as if being interrogated – yes, no, I don't know, I don't understand the question – but insists that he enjoys being interviewed. Indeed, his insistence that he enjoys being interviewed is one of his more verbose responses: "Yeah. It's like therapy for me. It's like making a record, right? I'm the artist, you're the producer, we're making a great record here!"

But then, has any interviewer not left Brian Wilson's presence at least slightly disconcerted or confused? Perhaps in the early 60s, when music seemed to gush out of him in an unceasing torrent, songs so dazzling in their perfection that the Beach Boys became enshrined in the public imagination as the living embodiment of the perfect Californian youth they sang about, despite a lot of physical evidence to the contrary – the almost unnecessarily handsome Dennis Wilson was hidden behind the drums, which left audiences looking at his two chubby brothers Carl and Brian, his balding cousin Mike Love and the diminutive, jug-eared guitarist Al Jardine.

Eventually, however, Brian Wilson had a nervous breakdown brought about by his incredible workload – between 1963 and 1965, he wrote and produced nine Beach Boys albums and 16 singles – and he began dosing his already fragile psyche with LSD in the pursuit of ever greater artistic achievement. The latter was a decision that, as he notes, had decidedly mixed results. "At first, my creativity increased more than I could believe," he says: he made Good Vibrations, a single remarkable even by his standards, and with Van Dyke Parks began working on Smile, the album that was supposed to be his masterpiece. There's a pause. "On the downside," he frowns, "it fucked my brain."

In truth, if you'd been listening closely, you might have realised something was up with Brian Wilson long before the events of 1967. Behind all the bragging and bravado of the Beach Boys' biggest hits – "We always take my car coz it's never been beat, and we've never missed yet with the girls we meet" – a strange, rather desperate sadness kept seeping out on B-sides and album tracks: In My Room, Please Let Me Wonder, In The Back Of My Mind. You could hear it on Wilson's instrumental introduction to California Girls, its gorgeous, autumnal wistfulness at odds with the song's sunkissed lechery; and it seemed to have overwhelmed the band entirely on 1966's Pet Sounds, an impossibly sumptuous album on which even the most upbeat songs were shot through with yearning and loss and confusion.

After it was released, Wilson says today, John Lennon rang him and told him it was the greatest album ever made, an opinion that would be repeated again and again in subsequent years. The rest of the Beach Boys weren't so keen. "They wanted surf music, surf music, surf music," Wilson barks, banging the table for emphasis. There's another pause. "The sadness came from me. Came from my heart."

He barks that as well: in fact, he barks everything, speaking out of the side of his mouth, a legacy of the deafness in his right ear that allegedly resulted from the umpteen childhood beatings dealt out by his appalling father, Murry, who, he says, "brutalised and terrorised" his children. You don't have to look too deeply into the Wilson family history to work out where the sadness might have had its roots. But when I suggest that these yearning pleas for love or solitude might have something to do his father, a failed songwriter whose volcanic temper could be soothed only by music, Wilson looks utterly blank. "I don't understand the question."

But whatever his mental state beforehand, LSD wreaked unimaginable havoc on the 25-year-old Brian Wilson. He abandoned Smile unfinished, much to the relief of at least some of his fellow Beach Boys, most notably Mike Love, who was openly, vocally horrified by the music he'd made, and by Van Dyke Parks' strange, impressionistic lyrics. Wilson began hearing voices "saying derogatory things", telling him that he was finished and was going to die soon, a condition that continues to this day. "Every day," he nods. "A daily struggle." The voices were accompanied by black depressions and bursts of crippling, irrational fear. Fifteen years after they began, he was diagnosed with bipolar schizoaffective disorder: in the meantime, Wilson attempted to silence them himself with cocaine and heroin. Fifteen years seems a long time to wait before seeking help for such terrible problems, I say. He frowns again: "I didn't need help before then."

That isn't what contemporary reports suggested. Meeting Wilson in 2011 might be hard work, but by all accounts it is nothing compared with meeting him mid-70s. It was about that time that the Beach Boys, desperate for a hit, announced that their errant mastermind was miraculously cured and sent him out to meet the press to prove it. The resulting profiles were heartbreaking and horrifying in equal measure, depicting a halting, visibly terrified man who said he "felt like a prisoner": occasionally, the interviews concluded abruptly with Wilson asking the journalist for drugs. Equally, I can be thankful I didn't meet him in the 80s, when he re-emerged again, looking movie-star handsome in a way he never had at the height of his fame, but with the ominous figure of Eugene Landy in tow, a therapist who had apparently nursed Wilson back to health at a cost of $35,000 a month, but who had also announced himself his manager, co-writer, producer, financial partner and beneficiary in all of Wilson's professional activities, and to whom Wilson had an alarming habit of referring as his "master" ("And a good dog always waits for his master!" he announced cheerily to one dumbstruck hack).

Eventually, Landy lost his psychologist's licence and found himself subject to a court-ordered removal and restraining order (he died in 2006). And thus Wilson's unexpected artistic Indian summer began, largely guided by his second wife, Melinda Ledbetter, a former car saleswoman he married in 1995 and with whom he's subsequently adopted five children. "His life turned into a better place," says Van Dyke Parks, "when he got a life companion, when he met that girl, his wife. Well, for better or worse, but certainly for richer not poorer, he's had a great life."

His solo career really took off in 2002, when he performed the Beach Boys' Pet Sounds live in its entirety at London's Royal Festival Hall, an event that was greeted with a kind of disbelieving hysteria by critics and fans, and that spawned a kind of mini-industry in its wake: you currently can't move for artists performing "classic" albums in their entirety. Since then, he's completed Smile, and released four further solo albums of varying quality. He plays music every day, he says, and tries to write something every month, but the songs don't come as easily as they once did, he says, and a couple of years ago they stopped coming entirely. "I don't know why," he says, but it's something that didn't even happen at his lowest ebb: amid the bleakness of the early 70s, he somehow kept sporadically producing incredible songs: Til I Die, This Whole World, Sail On Sailor…

There's always touring, however. Wilson's touring schedule is fairly remarkable for any 69-year-old, let alone one diagnosed with bipolar schizoaffective disorder. As he says, it's nothing compared with his early 60s workload, which given how that turned out is probably just as well.

But amid the critical acclaim and rapturous audiences, there are dissenting voices, who have noted Wilson's occasionally uncomfortable onstage presence – he suffers from stage fright, he says, a state of affairs compounded by the fact that the voices he hears get louder when he's onstage. And not for the first time in his career, there has been criticism that Wilson is being exploited. It's a charge denied by Jeff Foskett: "I think a lot of record companies took advantage of everybody out there in the 60s. But how do you recover from that? You do exactly what Brian has done: you forge on. In my opinion, the best part of Brian is that he's never cared about having a Rolls-Royce or a huge mansion or a beachfront property, he's only cared about how great a song he can write."

The problem, he says, is less with Brian Wilson than with other people: "When Brian Wilson's in a room, people don't know how to approach him."

Foskett thinks that his latterday career has been therapeutic. "It was obvious that he was having some memories, and they weren't necessarily the best memories, when we started to rehearse Smile. I think that he really loved it when he finally heard it performed live. I think it absolutely did exorcise those problems. It was therapeutic, even for me to watch."

Their relationship began in the mid-70s, when Foskett simply turned up at Wilson's Bel Air home unannounced, desperate to meet his hero, unabashed by the lurid stories that surrounded him. In any case, he says, he didn't find the bedridden, unwashed, irreparably damaged tragedy of popular myth. "I knocked on the door and Brian answered and said, 'Come on in.' We hung out, we jammed for an hour, we had some lunch and then he said nice meeting you, stay in touch. And I did. I think God really wanted it to happen." Eventually, Foskett ended up in the Beach Boys' 1980s touring band: "I think it was some of the more serene times for the band," he says, which seems an odd way of describing a decade in which it's widely thought that the saga of America's Favourite Band finally tipped over into the realms of soap opera: quite aside from the business with Brian and Dr Landy, Dennis drowned a few months after fathering a child by a woman alleged to be vocalist Mike Love's illegitimate daughter. Love did his bit to add to the ongoing weirdness by accepting the band's induction into the Rock And Roll Hall Of Fame with a rambling speech in which he variously attacked Paul McCartney, Diana Ross, Bruce Springsteen, Billy Joel and called Mick Jagger a "chickenshit".

"Well, Dennis did die unfortunately. But was it a positive experience? Absolutely. Brian was there on and off, he wasn't in great shape at the beginning, but by the end he looked great, he was physically sound. It was fun having him around."

In fairness, it was probably less turbulent than the 1990s, which the Beach Boys largely spent suing each other over songwriting royalties, the rights to the Beach Boys name and the contents of Brian's Landy-era "autobiography" Wouldn't It Be Nice, which it later transpired Wilson had never actually read, let alone written. Most of the litigation seemed to stem from Mike Love: when his most recent legal claim – that Wilson's promotion of the finished Smile album "shamelessly misappropriated Mike Love's songs, likeness and the Beach Boys trademark as well as the Smile album itself" – Rolling Stone gleefully reported it with the headline: "Brian Wilson finally defeats one of Mike Love's dubious lawsuits." By the end of the decade, Brian Wilson had left the band, as had vocalist Al Jardine, Carl had died of cancer, leaving Mike Love the sole original member, alongside Bruce Johnson, drafted in to replace Wilson after his mid-60s breakdown. More recently there seems to have been a thaw in relations. "I haven't spoken to Bruce Johnson in years, wouldn't even know what he looks like now, but I speak to Mike Love on the phone," Wilson says. "It's friendly although…" He searches for the right words. "No one wants to put their foot in the fire too long."

Still, Love seems to have unexpectedly overcome his animosity to Smile, declaring that a forthcoming box set of the Beach Boys' original sessions for the album features "cousin Brian at his creative peak… I'm unaware of anything that comes close in popular music." When I read this quote to Wilson, he looks blank. Doesn't he find it odd? "No. Why?" Van Dyke Parks is a little more effusive, or at least he is when finally he stops laughing. "I'm just incredulous. I can't believe that he's an enthusiast. I wouldn't condemn him if it took him some time to come to that conclusion. I'll just say that they have an expression in Texas that goes along with such a delayed reaction and that is: he's a little slow out of the shoot. All hat and no cowboy," he says, before dissolving into laughter again.

There is tentative talk of a Beach Boys reunion next year. Until then, there's more touring and another solo album, this time of Disney songs. When Wilson's not working, he says, he walks a mile and a half a day and listens to a local oldies radio station. He sees a psychiatrist: "He's like a friend. He asks me, 'How's the family?' He's like a guy I pay to be my friend." His young family exhaust him. What makes him happy? "Music."

After meeting him, I don't feel I'm any closer to understanding how anything in Brian Wilson's world works or worked – not the astonishing, nonpareil burst of 60s creativity, not his latterday renaissance – but I can't think of anything else to ask, or at least I can't think of anything that won't just elicit a yes or a no. If nothing else, in an age when rock stars are driven to tell the world everything, Wilson is going to go to the grave with his sense of mystery utterly intact. "Thank you for a wonderful interview," he barks, signs my copy of Pet Sounds and heads for the door.

• Brian Wilson tours the UK from 10 September. For more information, go to livenation.co.uk.