Marco Roth grew up with a secret: that his father had contracted HIV while conducting important medical research. But after his father's death, that story began to unravel – and with it everything he thought he knew about his family

Exactly how I found out about my father's illness keeps melting back into a fog of memories. In one version, I'm interrupted while reading a letter from the girl I'd kissed a few weeks before. In another, my father is at his place at the kitchen table, opposite my mother, who holds a napkin to her face. In the latest version, my father tells it as a bedtime story, as if I were a small child.

"Once upon a time," my father says, "when you were about five or six, I was working on an idea I'd had for a new malaria drug. I was also supervising the sickle-cell clinic at Mount Sinai hospital, and most of the blood we used for experiments was taken as samples from our sickle patients. One day, as I finished drawing blood from one of the regulars, I did something very stupid. I wasn't wearing latex gloves and, as I was about to get the needle out of this guy's arm, he jerked and the needle came out and poked me in the wrist, just below a vein. It was in for no more than a second or two. Now this guy had a lot of problems, not just sickle-cell disease, but, like a lot of the patients, he'd got hooked on heroin to get rid of the pain. You remember that's when I came down with hepatitis; you were too little for me to tell you about it. But at the time we were beginning to hear about this new disease…"

I didn't really find out in any of these ways. But however it went, just before I started high school I learned that my father had at some point contracted HIV, now had full-blown Aids and, according to him, had anywhere from zero to five years to live. There was one more thing that was impressed upon me: I mustn't tell anyone.

"I could lose my lab," I remember him saying to me once, perhaps when I'd asked if I could tell my favourite English teacher. "Is that what you want? The hospital wouldn't want the publicity or the risk. You have no idea what people will say."

That first year of my father's Aids, our kitchen transformed into a medical school cafeteria and a sort of war room where we followed the course of the illness. Blown-up photographs of lesions wound up on the table, a few places from where we ate spaghetti bolognese. My father and I practically dared each other to eat while looking at electron microscope slides of nematodes. My mother left the table in protest, her food untouched.

Even as my father was dying, he'd talk to me about the potential of the next generation of drugs in development. And then he'd add, "I won't make it that long" and, "Don't worry, I won't become a vegetable either." Late November, my second year of university, almost too weak to stand, nearly blind, my father felt a pain of uncertain origin. The only thing that could stop it, for a time, was Demerol (also known as pethidine), which my father recognised as the beginning of a cascade toward semi-consciousness. After Demerol would come morphine, and after morphine either prolonged coma or death. He wasn't about to find out which. The pain lessened for a day, two days, and then returned. At night, he began to take the morphine.

December's first Friday morning, the phone rang in my room. "I think this is it," my mother said. "You'd better come."

My father greeted me from the couch where he'd taught me to read. Ever the scientist, he explained: "Sodium cyanide can take you one of two ways. When it enters the heart, it causes almost immediate cardiac arrest, a heart attack. Everything stops. If your heart muscle is relaxed, it's a very peaceful death; they say painless. If your heart is pumping blood out and contracted, the body goes into a seizure. It's a 50-50 chance."

"Do you want me to stay?" I asked.

"No, no, don't stay. They might arrest you."

"For what?"

"You can't kill yourself in this country. It's illegal."

I hugged him, which it seemed I hadn't done for years. One of my arms could now reach almost entirely around his torso. I feared breaking something. Someone was trembling. I couldn't think of anything to say. "I'll miss you," I came out with, finally. It was a borrowed line, what my girlfriend and I had started saying to each other instead of "I love you", since maybe that was closer to the truth.

"I miss my mother every day," my father said. His last words to me.

Five years after my father died, his older sister, Anne Roiphe, a novelist and essayist, began work on her 13th book, a memoir about her childhood. The few times I'd tried to imagine my aunt typing at her small desk in a corner off her kitchen, I'd felt this shadowy fear. My father, my mother and I were becoming characters in someone else's drama. Then it happened. A copy of the book, 1185 Park Avenue, thumped through the letter box.

There were books that had changed my life, usually in subtle ways, such as The Ambassadors or To The Lighthouse. This was not that kind of book. The scenes exploded on my consciousness. They seemed to require some immediate action, but I wasn't sure what it was.

"He did not tell me he was sick until nearly a year and a half after he had full-blown Aids pneumonia and then he swore me to deepest secrecy," Anne wrote of my father. "Of course I considered the fact that I might still not have the full truth. If he did not, even then, tell me everything about his life and if his Aids was in fact contracted in the more usual way I would have been heartbroken – heartbroken because he would have lived so long bending beneath the deceptions forged in other ignorant and cruel times."

I stumbled over these sentences. Why would anyone write such a thing in a "non-fiction" memoir? She was outing him without outing him. There was a safety in that otherwise superfluous "in fact". Was Anne trying to avoid the truth of my father's obvious bad luck? Or did she know more than she let on?

It had never occurred to me to doubt my father's version of events. I had nothing really to oppose my aunt's suspicions except my own partial memories. But her descriptions of my father seemed like secondhand borrowings from Freudian studies of homosexuality. There was his ambivalence about supposedly manly pursuits and his turn to supposedly effeminate things such as music and literature. Even if these caricatures were sometimes true, just because many gays liked opera did not mean that all opera lovers were gay.

I said something like that last sentence to my aunt when, after pacing up and down my apartment for a while, I realised at last that I was going to have to call her.

"This was not the book I set out to write," she began, and for a second I thought she was preparing an apology. "I went to my publisher with an idea of writing about hero scientists, about my brother as a heroic scientist. People who give up their lives in the course of their research." She went on, more defiantly, it seemed: "So I began to research that book. I talked to people, people who knew your father. They told me certain things and I was reminded of other things I'd forgotten. And the story I wanted to tell started to seem wrong. It wasn't the story of his life."

"But what is the story?" I asked.

She wouldn't tell me. She had promised to protect her source, she said. I told her it seemed only right that I should know what she knew. She said she would ask. We left it there.

I knew I'd have to ask my mother, so I arranged to meet her for lunch. She had not been sent a copy of 1185 Park Avenue, she said, so I showed her the passage. She read it slowly.

"Is there anything to this?" I asked.

"Not as far as I know," she said.

"Do you believe it?"

"Dad loved you, loved both of us…"

"That's not the point," I interrupted. The way she called him "Dad" had already set me off, as though she thought I was still incapable of understanding that the man she married and my father were the same person. And really, why would my father's putative bisexuality have anything to do with whether he loved us? "Do you think it's true?" I asked again.

"You know as much as I know."

'There were things, my mother said, that no child ought to know about his or her parents, that were none of my business.' Photograph: Reed Young for the Guardian

Not long after this, my aunt called to say she'd spoken with her source and he'd agreed to talk to me. Victor was my father's closest friend and his boss, the hospital's chief of haematology. He said he'd made a strategic error. He'd told Anne two things he thought would keep her from writing any book about my father at all. The first was that the probability of contracting HIV via needle-stick infections in the lab was very small.

The second was an anecdote. One night in the early 1980s, while he and my father were at a conference in Chicago, Victor was relaxing in his hotel room when my father called and asked him to come out for a drink. Victor was tired and begged off. A few minutes later, the phone rang again, my father calling back to tell Victor he should come. He was at a gay bar, he said. It would be a new experience for him. Victor said he'd joked with my father about how he'd ended up there, and declined politely. He had to catch a flight the next morning. That was it. He thought nothing more about it. The invitation had been both unprecedented and never repeated.

A gay bar! That was it? I had been to gay bars. It did not make me gay. And the low probability of the accidental needle-stick infection? It was low probability, not impossibility.

I phoned my aunt to tell her I'd spoken to Victor. "It's nothing," I said. "Circumstantial evidence, that story about the gay bar."

There was a silence before she spoke. "He's your father as well as my brother. One day you'll tell the story in your own way if you want to."

My father had been dead 13 years, and my aunt had written four more books in the seven years since her memoir was published. It was a year and a half since my wife had given birth to our daughter, and four years since I'd consigned to a trunk the notes for my promised counter-memoir. I was up in New York in late January, ostensibly to help out with the magazine I'd started with friends from graduate school, but really because I needed a break from my marriage.

I'd accepted my mother's invitation to stay at her new apartment, three blocks from my aunt's. I arrived early, and she jumped when I greeted her. She was in the middle of writing a condolence note for Anne's husband, my uncle. He'd had a heart attack. This was to be her first communication with my aunt since the publication of 1185 Park Avenue.

After my father's death, my mother and I had become connoisseurs of the condolence note. We'd scrutinised them for signs of the writer's motives. "I'm sorry to hear about your loss…" meant that the writer wasn't sorry for the death but for getting news of it. Most of the notes we got began with expressions of shock. This hadn't been surprising, since fewer than 10 people had known about my father's illness. There were old friends who were hurt to realise that they had been out of the loop, and they told us so, as if my father's death had wronged them.

Our favourite genre of condolence note was the one that recalled some detail of my father's life, an anecdote from his medical student days or his college years, or recorded my father's kind acts: his care of a particular patient, his vigorous promotion of his former lab technician who'd gone on to become a successful researcher.

I recognised my mother's note as intended in this last style. Even so, that genre no longer seemed appropriate. With the history between them something more was required, or nothing at all.

"You're still angry at her?" My mother looked at me and nodded. Whatever it was in that look of hers, fear or guilt, something no longer made sense to me. How could one be enduringly angry at someone who did not, in the end, have either right or power on their side? My aunt was a fantasist, a novelist. The unprovable speculations she'd published about my father were years behind us. No one seemed to have made anything of them, or cared much, really, whether my father had got Aids in the more usual way or not. At least, no one cared about it apart from us.

I asked again the same question I'd asked years before. Or rather, I asked it in a different, more direct way: "Were you telling me the truth?"

Instead of answering, she asked if I wanted to go for a walk. We were halfway around the block before she started, at last. "Dad loved you, loved us…" she began, as she had before. And, as before, I cut her off. "That's not what I asked." We walked on in silence. Then she plunged in again. "In, I guess, 1976, you were about two, Dad, Gene, your father, told me he'd been… sleeping… with a man, but that he'd stopped and it was the last time. Maybe he kept his promise, maybe he didn't. Maybe that was the truth, maybe that wasn't the whole truth… When you asked me before what I knew about how he got Aids and I said, 'I knew what you knew', I was telling you the truth."

She seemed unsure what voice to use, whether she should speak as a mother, reassuring the boy I no longer was about a father who had been gone a while, or as though confiding in a sceptical friend. "I knew when I married him, but I can be very stubborn," she said. And, at last, with a sigh, almost of impatience: "I thought you really always must have known."

Had I been stupid, blundering and insensitive? Up rose a flash of memory showing me my father reading the gay British historian AL Rowse's Homosexuals In History. It was tented open, the front cover a photo of Michelangelo's David, glorious nudity right there on the bed. Right there an invitation, perhaps, for me to ask why he was reading it. I had filed it under general culture, the library of every civilised person. I had missed everything, missed my parents' lives.

We went back to the new apartment which, more than ever, struck me as a condensed version of our former one, a miniature museum to a past that seemed nothing but a hoax. The dinner things were still out on the table, untouched. I picked up a half-full glass of wine, twirled it, and hurled it against the wall. Then dutifully, but without any real remorse and even a certain feeling of relief, I swept up the fragments and vacuumed the shards and sponged the wall clean.

My mother was glued wordlessly to an armchair. She'd obviously just done, for her, an enormously brave thing, one of the bravest in her life. She must have known she was taking a huge risk in telling me. Not only disgorging a painful secret that she'd kept faithfully for years, but also admitting her earlier lie.

There were things, she said, that she believed no child ought to know about his or her parents, things that were, essentially, none of my business. It was, she repeated, her life. Before my eyes, she was retreating back to where she'd been before, as if once the glass were cleaned up we could simply go on forgetting about it.

I awoke the next morning thinking everything had changed. And yet nothing changes right away, at least not dramatically. Of course I could have decided to go looking for more concrete proof of how my father had contracted the disease, although the odds of finding anything definitive seemed very poor. I could no longer talk to Victor, who'd succumbed to early-onset Alzheimer's. I pictured myself walking around New York like a private investigator carrying a picture of my father from the 1970s – "Have you seen this man?" – tracking down former frequenters of the clubs close to the clinic where he had worked. Except that the clubs, too, were gone, along with most of the people who'd frequented them, including whoever might have passed the disease on to him.

Perhaps, after all, my parents' arrangement had suited them. Perhaps if there'd been no HIV, my father would have gone on, more or less happily, in his double life, flown off to Morocco for some conference and brought back a pair of camel-hide slippers for me, an inlaid silver bracelet for my mother and his own memories. Or he might have come out of the closet, eventually, when I was a teenager, moved in with a young Asian violinist a little older than I was, and I would have become ferociously jealous, gone off on some confused, gay-bashing prank, and ended up embittered in a totally different way. There were myriad possible variations, but only one real outcome. I'd been the child of their denial. I knew that now.

• This is an edited extract from The Scientists: A Family Romance, by Marco Roth, published by Union Books at £14.99. To order a copy for £11.99, including UK mainland p&p, go to guardian.co.uk/bookshop.