On 3 December 1572 William Charke left Peterhouse and walked up Trumpington Street towards Great St Mary's, the University Church. The route was familiar; Charke had been a member of the University of Cambridge for twelve years. He had arrived, little more than a boy, short of funds and good breeding, but he was gifted and he had worked hard. He had made friends and earned a bit of dignity. By December 1572 he had been a fellow of Peterhouse for six years, and he left the college that day clutching the text of a Latin sermon that he was to preach to the university. It is to be hoped that he had a sense of occasion and enjoyed his short walk. This was the finest moment of his Cambridge career; it was also the end of that Cambridge career. Later, he claimed that he was surprised that he had upset a learned audience, listening to a Latin sermon in a university town. In truth, however, the sermon was breathtakingly offensive and Charke knew it. He had preached about bishops and archbishops. According to The Book of Common Prayer, bishops exist for the edifying of the Church and for the honour, praise and glory of God. Charke however thought that they were sent by Satan and said so. His sermon was a blistering attack on prelacy and on the assumption that some ministers might be superior to others.

The day after the sermon, the journey up Trumpington Street had to be repeated. This time, though, Charke was on his way to the university court, newly established in what had been a waiting room in the Schools building, just a stone's throw from the University Church. The Vice-Chancellor and several of the heads of house were waiting for him. Charke was in very serious trouble, but he was defiant and unrepentant. In fact, when the heads suggested that an apology would be welcome, he spoke to them ‘in very unseemly manner and with taunting words’. He was given time, rather a lot of time, to think again, but he remained defiant and on 5 February 1573 he was expelled from the university. The Vice-Chancellor and heads could make no accommodation with someone so ill at ease with the Church of England. Rather surprisingly, given that he had seemed to invite this punishment, Charke was dismayed.