Cooper was again elected for Wiltshire for the parliament of 1656, but Cromwell refused to allow him, with many others of his opponents, to sit.
In the prolonged discussions regarding the Bill of Indemnity he was instrumental in saving the life of Haselrig, and opposed the clause compelling all officers who had served under Cromwell to refund their salaries, he himself never having had any.
In 1653 he returned to London, and having denounced Cromwell for accepting the office of Lord Protector he was imprisoned.
In 1643 Cromwell performed one of his earlier exploits in taking Lowestoft, capturing large supplies and making prisoners of several influential royalists.
As early as the beginning of the 9th century Ameland was a lordship of the influential family of Cammingha who held immediately of the emperor, and in recognition of their independence the Amelanders were in 1369 declared to be neutral in the fighting between Holland and Friesland, while Cromwell made the same declaration in 1654 with respect to the war between England and the United Netherlands.