How did Samuel Pepys defend himself against the accusations involving Sir Edmund Berry Godfrey?

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Diarist Samuel Pepys — Samuel Pepys Samuel Pepys, oil painting by John Hayls, 1666; in the National Portrait Gallery, London.

Samuel Pepys defended himself against accusations involving the murder of Sir Edmund Berry Godfrey by producing an "unanswerable alibi" when Lord Shaftesbury attempted to implicate him in the crime during the Popish Plot.1

When his enemies subsequently tried to link him to the murder indirectly by accusing his confidential clerk, Samuel Atkins, Pepys also successfully provided an alibi for Atkins, preventing his likely execution despite the use of third-degree interrogation methods against him.1