Although the murder of the magistrate Sir Edmund Berry Godfrey, which sparked the Popish Plot, has never been solved, a strong body of evidence points to Pembroke as the killer.

From childhood on, especially when drunk, he was subject to fits of violence: he may have inherited his mental illness from his grandfather, the 4th Earl, who had been notorious for his sudden and unprovoked attacks on fellow peers.

On 28 January 1678, Charles II, not a man easily shocked, committed him to the Tower of London "for uttering such horrid and blasphemous words, and other actions proved upon oath, as are not fit to be repeated in any Christian assembly".

Pembroke submitted a petition to the House of Lords for their assistance, denying everything alleged and praying that his fellow peers "will not believe the accusation, or your petitioner capable of so horrid a crime".

However, by then Pembroke had already killed a man, Nathaniel Cony, whom he knocked down and kicked to death in a tavern for no apparent reason, and a few days later a Middlesex grand jury indicted him for murder.

[5][6] The Lord High Steward, the Duke of Ormonde, who presided at the trial, warned Pembroke that "his lordship would do well to take notice that no man could have the benefit of that statute but once".

On 17 October 1678 Sir Edmund Godfrey, who had been foreman of the grand jury which indicted Pembroke for the murder of Nathaniel Cony, was found dead in a ditch on Primrose Hill, impaled with his own sword, and this unexplained death caused an anti-Roman Catholic uproar, generally known as the Popish Plot.