Cromwell summoned a second Parliament in 1656, although the hundred members who had resigned over the "Recognition" were excluded from elections. When the new members of Parliament arrived in Westminster in September, Cromwell greeted them with a stern speech full of anti-Royalist and anti-Catholic rhetoric. Cromwell warned the new members of the "enemy within," urged them to fight for the Reformation, and spoke of the threat of an imminent Spanish invasion. Despite Cromwell's pessimism, however, his second Parliament as Lord Protector proved very cooperative. Few of the members objected to the exclusion of the hundred members who had resigned earlier, and the House passed an act nullifying Charles Stuart's right to the crown. Parliament showed strong support for war with Spain, and even voted in favor of subsidies to prepare the army and navy in case of an invasion. The House was also more willing to support Cromwell's civic reforms. Among these were the regulation of alehouses, the provision of work for the poor and unemployed, and the regulation of "undecent fashions" for women.

Parliament's opposition to Cromwell's push for religious tolerance and to the maintenance of a standing army did not subside, however. Furthermore, the conservatives continued to push for a constitutional settlement that would put some sort of hereditary office at the head of the government. For a time, Cromwell refused even to consider providing for a successor to his title, but in February 1657 he finally gave his approval to having the issue debated in the House of Commons. At the end of March, the members of Parliament presented Cromwell with what was called the Humble Petition, which contained Parliament's proposals for the settlement. The Humble Petition contained a number of provisions, among them an outline for a limited, hereditary monarchy. The petition also endorsed the principle that Parliament should approve all the great officers of state as well as all new taxes, and called for a recreation of the House of Lords, which had been abolished alongside the monarchy, whose members would be nominated by the Lord Protector and his Council. The Humble Petition offered Cromwell the crown, and he agonized over whether or not to accept the title for five weeks. Eventually, Cromwell turned down the chance to be officially named King, a title that would have passed to his eldest son upon Cromwell's death.

When Parliament came back into session in the fall of 1657, it proved to be less cooperative than the parliament that had passed the Humble Petition. In this later session, the hundred members who had previously been barred were permitted to return, and they continued their fierce opposition to Cromwell. Furthermore, some of Cromwell's former allies–Independents like Wharton, Saye, and Sele–declined his invitations for cooperation. In January 1858, renewed opposition from the republican members of Parliament further upset Cromwell's plans for the government. A republican-inspired petition calling for the abolition of the Protectorate and for the rule of a single-house Parliament found great support in London, particularly within the army. The day this petition was to be presented to the House of Commons, Cromwell rushed to Westminster and permanently dissolved Parliament.

The last few months of Cromwell's life were marred by family tragedies and further political unrest. One of his sons-in-law, Robert Rich, died in late February, and Cromwell's favorite daughter, Elizabeth Claypole, died of cancer in August 1658. During the months of his daughter's illness, Cromwell lost much of his spirit, and his own health began to suffer. His health and state of mind were not helped by a renewal of Royalist plotting in the spring and summer of 1658, and he dealt with this new intrigue ruthlessly, appointing a High Court of Justice to try all conspirators and hang many of them for treason.

Around this time, Cromwell's eldest son, Richard, was brought from his estate in Hampshire in preparation for his succession to the office of Lord Protector. This period of preparation lasted only a few months, until Oliver Cromwell died of pneumonia on September three, 1658. His effigy lay in state for many weeks afterwards, and large crowds gathered to pay respects or simply to look at the "great man." Only two years later, however, with Charles Stuart restored to the throne as Charles II, Cromwell's legacy would change. By 1660, he was known as the "great bad man," and his corpse was dug up from its grave and hanged publicly at Tyburn.

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