The contention brought to a crisis the struggle between the moderate Presbyterians and the Scots on the one side, who decided to maintain the monarchy and fought for an accommodation and to establish Presbyterianism in England, and on the other the republicans who would be satisfied with nothing less than the complete overthrow of the king, and the Independents who regarded the establishment of Presbyterianism as an evil almost as great as that of the Church of England.
As the recognized leader of the new party, his nomination by the Republicans for the presidency in 1856 and in 1860 was regarded as certain; but in each instance he was put aside for another.
When the republicans triumphed Martos retired into exile, and soon afterwards into private life.
After the 28th of December 1654, he left the privy council, and henceforward is found with the Presbyterians and Republicans in opposition to Cromwell.
The court accused him of being at the bottom of every popular movement, and saw the "gold of Orleans" as the cause of the Reveillon riot and the taking of the Bastille, as the republicans later saw the "gold of Pitt" in every germ of opposition to themselves.