One single incident serves as a perfect illustration of just what an extraordinarily unusual and charismatic person the US musician Frank Zappa, who died in 1993, must have been. In 1968, a year that saw the assassinations of Martin Luther King and Bobby Kennedy, a man turned up on the doorstep at the Log Cabin, the ramshackle, open-all-hours-to-all-comers crash pad in Laurel Canyon, Los Angeles, that Zappa and numerous other weird people called home. "My name is Raven. I brought you a present," this stranger announced, handing to Zappa a transparent bag, apparently filled with blood, before pointing a revolver at his chest.

Calmly, Zappa cajoled and manipulated Raven into walking with him, and numerous spectators, including Zappa's 24-year-old English secretary, to a nearby lake. He then persuaded everyone present to start throwing things into the water, including Raven, who threw in his gun. The secretary, Pauline Butcher, threw in a twig, which "floated on the algae" causing her to look round "apologetically". After that, Zappa, shoved the bag of blood back into Raven's hand, saying: "You must leave now." Raven did. Immediately exhorted by the many witnesses to call the police, Zappa refused. Why? "Because if I call the police, the police will arrest him and he'll go to jail and no one deserves to go to jail."

For Butcher, who worked for Zappa at the Log Cabin, and lived there too, this was just another gesture of outrageous and frustrating anti- authoritarianism from a man who was full of such gestures, a man who, nevertheless, she admired to the point of worship. Now, 40 years on from her time as Zappa's live-in assistant, Butcher has written a book, Freak Out! My Life With Frank Zappa, offering a detailed account of what she now understands to have been the two most remarkable – and marketable – years of her existence.

Looking at Butcher now, at this the casually but carefully dressed woman in her 60s, as she nervously sips sparkling water in the Royal Garden Hotel, in west London, the experiences she describes in her memoir seem hard to believe, very far from the life that she lives now, as Mrs Bird, with her husband, a banker with Rothschild's, in Singapore. But that life is not so far away, not today, anyway. It was in this hotel that Butcher, at 23, first encountered Zappa, when she was sent by her stenographic agency to transcribe and type up some lyrics for him. Here she sits, fretting about what the survivors among those who lived or hung out at the Log Cabin during those two years might think of what she has written about them.

Not very long after her first few meetings with Zappa, Butcher moved to the US and became his full-time secretary, despite the lack of convention with which the role was first suggested to her: "Do you think if we fucked, you could still work for me as my secretary?" Zappa asked. Butcher declined intercourse, although at that point she was certainly nurturing romantic thoughts about him. She was upset when she turned up in the US – pretty much on the strength of this most slender of invitations – and discovered that Zappa had a wife and a baby son. All the way through their strange relationship, Butcher declined to have sex with "Frank", even though Mrs Zappa – Gail – did not believe this. Gail eventually confronted Butcher with her suspicions while "researching" a book about her husband's many groupies, of whom she had been one herself. That book, never written, had been Zappa's idea. He was obsessed with groupies without musing too much on the inequality inherent in the relationships. So what the hell did this young woman think she was doing, immersing herself in this life so different from her own, and in some respects, so repulsive to her? Butcher still doesn't know. For her, it was all about "Frank" and still is. What Butcher is still pondering is this: "What was his motivation in asking me to go there?"

Butcher admits that her life in London was "pretty dull". She wore minis, and drove a Mini, but actually spent little time doing anything other than working hard as a typist and as an instructor at the modelling school she'd attended, teaching credulous, hopeful girls like herself, girls without quite enough beauty to make it in modelling, whatever instruction they purchased. Certainly Butcher hoped that she would get "a break" from her association with someone who was famous. She nurtured her own ambitions to be a writer even then, ambitions that Zappa encouraged. But she was also intensely devoted to Zappa. "I was besotted with him. I was aware that he was something unusual. I don't think I was in love with him. I agree with his ideas about romantic love, that it was overplayed."

Butcher also believes that Zappa wasn't really "like" the life that he lived. "Underneath it he was a very conventional character. I couldn't have done it with the others around at that time – Rod Stewart, Jeff Beck, those crazy people, who took drugs." Drug-taking, notably, was something that Zappa could not tolerate.

In the world of rock biography, fandom is exploited heavily. Pretty much anyone who can lay claim to some level of articulacy, and who has a modicum of provenance to offer, can find a publisher for their musings. When Butcher sent out her proposal, she received 12 expressions of enthusiastic interest right away. But Butcher's book is of wider interest. Sure, it describes a formative time in the life of an innovative musical artist, which Zappa most certainly was. But it also captures a particularly intense experience of a very brief, yet enormously influential, period in the evolution of western womanhood. Butcher worked for Zappa during the interstitial time between "sexual liberation" and "women's liberation". Zappa was a sexual libertarian and enthusiastic celebrant of "groupie culture", while his straight, conservative secretary was shocked and appalled by the sexual incontinence all around her, and the tensions in their relationship are instructive.

Butcher herself, rather charmingly, is almost entirely lacking in the desire to subject her observations to interpretive analysis, although she writes in huge detail, drawing on the numerous long letters she sent back home to England. "I was so ga-ga, at first, so shocked … I just observed it all and I loved writing home to my family, telling them every detail of it all."

But gradually she began to experience moments of clarity. When Butcher heard one of the "Mothers" – the members of Zappa's backing band, the Mothers of Invention – say he felt sorry for one groupie because she had been with three different musicians on consecutive nights, she became irritated, since the men who behaved that way were congratulated for "scoring". Or as she says, with understatement: "I began to notice the double-standard."

Butcher was upset when Zappa did not see her point of view. Something clicked in her mind when she saw feminist campaigners in the news. "I saw a banner that said: 'Love me less, respect me more.' And I just thought: 'Yes. That's it.'" Butcher read Kate Millett's Sexual Politics, which came as a revelation to her, as it did to many women at that time. Excitedly, she told Zappa what she had realised. "I thought he'd be sympathetic, but he wasn't, completely the opposite."

From there on in, developments conspired to fragment the group that had lived in the Log Cabin. Butcher herself says: "I didn't want to spend my life devoted to him. I found that people were only interested in my connection with Frank, and not in me. Once I left Frank, I never mentioned him again for years."

Butcher returned to England, went to Cambridge and did a psychology degree, married a fellow student, and began teaching. But when her husband moved from teaching to banking, and they had a son, she gave up her career for a second time. Bereft when her son left home and went to university, she decided to pick up her youthful ambition again, and write. She soon worked out that even after all those years, it was Zappa whom people were interested in. Butcher sees the irony: "The only story I could write that no one else could write was this one, about living and working with Frank Zappa."

She spent four decades trying, but Pauline Butcher couldn't quite shake her belief in Zappa, and his power to add glamour and interest to her life. In that respect, it's a sad story, this story, of the one who didn't, in the end, get away. But in other respects, the ending is happy. Pauline Butcher, the hopeful young woman who wanted to achieve something special and unique, finally did get her wish.