The following is the tale from the books. As you can see he states he want s to kill Stannis if he is a sorcerer too and if Varys' sorcerer is still alive I'd assume he'd still want to kill him too. However, no mention is made of Varys having captured the sorcerer to date.
"One day at Myr, a certain man came to our folly. After the performance, he made an offer for me that my master found too tempting to refuse. I was in terror. I feared the man meant to use me as I had heard men used small boys, but in truth the only part of me he had need of was my manhood. He gave me a potion that made me powerless to move or speak, yet did nothing to dull my senses. With a long hooked blade, he sliced me root and stem, chanting all the while. I watched him burn my manly parts on a brazier. The flames turned blue, and I heard a voice answer his call, though I did not understand the words they spoke.
"The mummers had sailed by the time he was done with me. Once I had served his purpose, the man had no further interest in me, so he put me out. When I asked him what I should do now, he answered that he supposed I should die. To spite him, I resolved to live. I begged, I stole, and I sold what parts of my body still remained to me. Soon I was as good a thief as any in Myr, and when I was older I learned that often the contents of a man's letters are more valuable than the contents of his purse.
"Yet I still dream of that night, my lord. Not of the sorcerer, nor his blade, nor even the way my manhood shriveled as it burned. I dream of the voice. The voice from the flames. Was it a god, a demon, some conjurer's trick? I could not tell you, and I know all the tricks. All I can say for a certainty is that he called it, and it answered, and since that day I have hated magic and all those who practice it. If Lord Stannis is one such, I mean to see him dead."
A Clash of Kings, Tyrion X
For completeness the following is the conversation from the show and as you can see it is very similar.
Varys: Before all this nastiness, I was going to tell you the story of how I was cut. Do you want to hear it still?
Tyrion Lannister: I don't know. Do I?
Varys: As a boy, I travelled with a troupe of actors through the Free Cities. One day in Myr, a certain man made my master an offer too tempting to refuse. I feared the man meant to use me as I'd heard some men used small boys. But what he wanted was far worse. He gave me a potion that made me powerless to move or speak, yet did nothing to dull my senses. With a hooked blade he sliced me, root and stem, chanting all the while. He burned my parts in a brazier. The flames turned blue and I heard a voice answer his call. I still dream of that night. Not of the sorcerer, not of his blade. I dream of the voice from the flames. Was it a god? A demon? A conjuror's trick? I don't know. But the sorcerer called and a voice answered. And ever since that day, I have hated magic and all those who practice it. But you can see why I was eager to aid in your fight against Stannis and his Red Priestess.
Tyrion Lannister: A symbolic revenge of sorts.
Varys: Yes, ahem. I feel the need for actual revenge against the actual person who tried to have me killed. Which will require a degree of influence, which-- You do not possess at the moment. But influence is largely a matter of patience, I have found. Once I had served the sorcerer's purpose, he threw me out of his house to die. I resolved to live to spite him. I begged. I sold what parts of my body remained to me. I became an excellent thief and soon learned that the contents of a man's letters are more valuable than the contents of his purse. Step by step, one distasteful task after another, I made my way from the slums of Myr to the small council chamber. Influence grows like a weed. I tended mine patiently until its tendrils reached from the Red Keep all the way across to the far side of the world where I managed to wrap them around something very special.
Tyrion Lannister: The sorcerer.
Varys: Hello, my old friend. It's been a long time. I have no doubt the revenge you want will be yours in time if you have the stomach for it.
Game of Thrones, Season 3 Episode 4, "And Now His Watch is Ended"