April 1647 he was twice sent to the head-quarters at Saffron Walden to persuade the soldiers to engage for Irish service, and attributed his ill-success to the influence of the higher officers rather than any genuine grievances among their men (ib. pp. 42–94; Clarke Papers, i. 6; Lords' Journals, ix. 152). By his opposition to the petitions of the army he earned its hostility, and came to be regarded as one of its chief enemies. In July 1647, when eleven leading presbyterian members of parliament were impeached by the army, Waller was accused not only of malicious enmity to the soldiery, but also of encouraging the Scots to invade England and of intriguing with the queen and the royalists (the articles of impeachment, together with the answer drawn up by Prynne on behalf of the accused members, are reprinted in the Old Parliamentary History, xvi. 70–116). At the end of July the London mob forced the parliament to recall its concessions to the army, and Waller was accused of instigating and arranging the tumults which took place. From all these charges he elaborately, and to some extent successfully, clears himself in his posthumously published ‘Vindication’ (pp. 44–106; cf. Recollections, p. 116). When the presbyterians determined to resist by arms, Waller was made a member of the reconstituted committee of safety, and ordered to attend the House of Commons, from which, with the other accused members, he had voluntarily withdrawn himself. On the collapse of the resistance of London he obtained a pass from the speaker and set out for France, was pursued, released by Vice-admiral Batten, and landed at Calais on 17 Aug. 1647 (Vindication, pp. 186, 201; Gardiner, History of the Great Civil War, iii. 349). On 27 Jan. 1648 Waller and his companions were disabled from sitting in the present parliament, but on 3 June following these votes were annulled (Rushworth, vii. 977, 1130). Returning to England and supporting the proposed treaty with the king, Waller was one of the members arrested by the army on 6 Dec. 1648, and, on the charge of instigating the Scots to invade England, he was permanently retained in custody when the rest were released (Gardiner, iv. 275; Old Parliamentary History, xviii. 458, 464, 466; Walker, History of Independency, ii. 39). He describes himself as ‘seized upon by the army as I was going to discharge my duty in the House of Commons, and, contrary to privilege of parliament, made a prisoner in the queen's court; from thence carried ignominiously to a place under the exchequer called “Hell,” and the next day to the King's Head in the Strand; after singled out as a sheep to the slaughter and removed to St. James's; thence sent to Windsor Castle and remanded to St. James's again; lastly, tossed like a ball into a strange country to Denbigh Castle in North Wales (April 1651), remote from my friends and relations’ (Recollections, p. 104; Cal. State Papers, Dom. 1651, p. 151). He remained three years in prison, untried and uncondemned. During the Protectorate Waller was in a very necessitous condition. The 2,500l. which parliament had promised to settle upon him he had never obtained. Winchester Castle, which was his property, had been dismantled by the government to make it untenable, and his estates had suffered considerably during the war. He possessed by grant the prisage of wines imported into England, but legal disputes prevented him benefiting by it (Cal. State Papers, Dom. 1652–3 p. 167, 1656–7 p. 269, 1657–8 pp. 62, 109). On 22 March 1658 he was again arrested on suspicion and brought before the Protector. ‘He did examine me,’ writes Waller, ‘as a stranger, not as one whom he had aforetime known and obeyed; yet was he not discourteous, and it pleased the Lord to preserve me, that not one thing objected could be proved against me; so I was delivered’ (Recollections, p. 116). These suspicions were not unjust; for Waller was already in communication with royalist agents, and in the spring of 1659 no one was more zealous in promoting a rising on behalf of Charles II. Charles expressed great confidence in his affection, and (11 March 1659) ordered Waller's name to be inserted in all commissions. Waller received this mark of confidence with effusion, kissed the paper, and said, ‘Let him be damned that serve not this prince with integrity and diligence.’ Some presbyterian leaders wished to impose terms upon the king, and Waller was obliged to support them, though assuring Charles that the first free parliament called would remove them (Clarendon State Papers, iii. 429, 437, 444, 446).
When Sir George Booth's insurrection broke out, Waller was again arrested (5 Aug. 1659), and, as he refused to take any engagement to remain peaceable, was sent to the Tower. He obtained a writ of habeas corpus, and was released on 31 Oct. following (Recollections, p. 105; Cal. State Papers, Dom. 1659–60, pp. 107, 135). Waller joined Prynne and the other excluded members in their unsuccessful attempt to obtain admission to their seats in parliament on 27 Dec. 1659 (Old Parliamentary History, xxii. 30).
