Pilkington was involved in the debate after the destruction of St Paul's Cathedral by lightning in June 1561. In the aftermath, he preached a sermon at Paul's Cross ascribing the destruction to the wrath of God and warning of worse to follow. The sermon provoked an angry response from a Catholic apologist alleging the cause was abandoning the old faith and blasphemy. Pilkington was rattled and responded with a "Confutation of an Addition" (1563), an uncompromising onslaught on the Catholic church.