When it became clear that it was not just defeat that accompanied the returning troops, but plague, Elizabeth left hurriedly for Windsor, and prohibited anyone in London from following. Soon no less that 1800 a week were dying in her capital city, and so she gave orders that anyone defying her travel prohibitions was to be hanged as an example to others. There, in Windsor and heavily pregnant, she prepared to brave it out, and to take the opportunity to ensure that no one but her very closest aides saw her. The plague slowly faded, and in September 1563, while I remained far away in France, Elizabeth gave birth to Dudley’s daughter, who she named after her mother, Anne.
Meanwhile, from early in 1563 Dudley’s inexorable rise had seemed to accelerate. By the summer he was being showered with lands, and in the autumn, with a Dukedom. You can imagine how I felt, but the reason for all this attention was not at all what I had thought. I finally heard the story from her late in 1563, when, after the birth of Dudley’s child in September, I gritted my teeth and
returned to England.
“We thought we would never see you again, Aly...” she said, “why did you abandon us?”
“Your majesty, I could see that Dudley was back in your favour,” I replied, trying to warm the coldness I felt, “and I feared that I would be in your way. Then, when I heard of the Edict of Amboise, I realized I was badly needed in France, and so departed urgently. I regret I did not have time to tell you of my plans, but I feared my family to be at risk in Lyons…”
“In other words, you were jealous of him.” It was not so much a question, as a conclusion. I remained quiet. “But then you stayed away the rest of the year… “we needed you and you were not there for us.”
“Your Grace…” I began, trying to think of a diplomatic way to say that on arriving in France I had heard that she was pregnant, and I knew it wasn’t my child…
“Aly,” she said, resting her hand on mine. I wanted to withdraw it, but dared not. I was shocked at my cowardice.
“Aly, did you not realize that we became pregnant by him against our wishes?”
“…against your wishes?” I was stunned. It had not occurred to me. ”Are you saying…!”
“He raped me, yes. I admit to having flirted with him, but that was usual in court, but he abused the trust I had in him. One night at Christmas he forced himself on me. I was beyond outraged, but what could I do? I could hardly have him arrested for it, could I, and go through the inevitable scandal of him denying it and saying it was consensual. I mean, that would be what the whole country would be thinking anyway… Even if I had come out of it looking like an angel, he would have been executed, and I needed him. He is the effective head of the Plantagenets, and I must keep him close to see what he is up to, and to stop him conspiring against me, and to do that I have to keep his hopes alive that we would marry.”
I was aghast. Could this be true? Her forgetting to employ the regal ‘we’ was more than unusual. I had noted her doing this before only in moments of intense emotion, so it seemed it could not but be what had happened. It had not crossed my mind that it could have been rape. “I’m sorry…”, I stammered, not knowing what next to say, but she interrupted me.
“So I had to keep him close, but I dared not incur the contempt of my people. Were the Spaniards to invade…” she sighed, and seemed to recover herself, “we would need the love of every last humble citizen to survive, so we didn’t want them to be upset or think us a harlot. But at the same time we had to find a reason for him to continue to be at court, hopeful. And then it occurred to us. Most likely you would have thought of it long before, but you weren’t here – you were sulking in France.”
She looked at me, clearly still annoyed, but I didn’t want to disrupt the flow.
“At the same time all this was going on, and we realized we were with child, we needed to find a way to keep Mary Stuart docile. How could we tame the Queen of Scotland? How could we make sure she could not easily take the throne of England from us - or if we died, and she somehow acceded to the English throne, turn the country again towards the tyranny of Rome? And then the answer came to us, as if from God. We had a proposal we could make, one that suited our needs perfectly. So we asked Dudley to marry the Scottish Queen, the terms being that he would become King of Scotland alongside her, and that all three of us would live together at our court here in England. She would keep him happy sexually, so we would not fear any repeats of the lewdness that happened before, and should she die he would remain King of Scotland, and there would be no chance of a return to Papacy.”
“You want Dudley to marry Mary, Queen of Scots!?” I was breathless, but not so breathless I couldn't add, with a little malice to burn the ice - “Oh, of course, Dudley has a way with unwanted wives, too, no?”

From  'Aly, Michelangelo's Son', Part 12 'Both Sides of the Coin'


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