When the elder Scrope died, Lowther expected to be re-appointed to the position by Thomas Scrope. He was incensed when Thomas appointed his brother-in-law, Robert Carey to the position.
When Jemmy Atkinson was found murdered in Carlisle with evidence linking his death to Barnabus Cooke and Robert Carey, Lowther arrested Cooke and tried to convince Carey to sacrifice Cooke and return to London. Carey refused and spoke at the coroner's inquest. I spite of Lowther's attempt to pack the jury, he lost in his attempt to blame Cooke and Carey.