Returning to Scotland in 1586 and mixing again in politics, Hamilton sought to reconcile James VI of Scotland with his mother; he was in communication with Philip II of Spain in the interests of Mary and the Roman Catholic religion, and neither the failure of Anthony Babington's plot nor even the defeat of the Spanish Armada put an end to these intrigues.
He was distantly related to Anthony Babington, who in 1586 was hung, drawn and quartered on Tower Hill for his participation in a plot to put Mary, Queen of Scots, on the English throne.
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After Parr's death in 1548, the house went to Sir Anthony Babington who was executed in 1588 for his part in the plot to kill Queen Elizabeth I.