On 5 March 1839 he brought in a bill for the registration of voters in Ireland (ib. 3rd ser. xlv. 1286). During the prolonged debate on Mr. C. P. Villiers's motion in the same month, O'Brien expressed his opinion that he ‘did not see that any advantage would result from the repeal of the corn laws sufficient to counterbalance the sacrifice of the agricultural interest’ (ib. 3rd ser. xlvi. 809–11); and on 6 May, much to O'Connell's disgust, he voted with Sir Robert Peel against the Jamaica Government Bill (ib. 3rd ser. xlvii. 971; Correspondence of Daniel O'Connell, edited by W. J. Fitzpatrick, 1888, ii. 177, 183–4). In this year a paper written by O'Brien, on ‘Education in Ireland,’ was published by the Central Society of Education (third publication, pp. 140–83, London, 8vo). On 4 Feb. 1840 O'Brien seconded a motion for the appointment of a select committee to inquire into the causes of discontent among the working classes (Parl. Debates, 3rd ser. li. 1234–6), and on 2 June he moved a resolution in favour of free emigration to the colonies (ib. 3rd ser. liv. 832–67). In February 1841 he supported the second reading of the Parliamentary Voters (Ireland) Bill (ib. 3rd ser. lvi. 867–9), and on 6 April strongly advocated the appointment of a minister of public instruction (ib. 3rd ser. lvii. 942–8).
During the debate on the address in August 1841 O'Brien warmly defended the whig ministry, and declared that it was ‘the first government that had made an approach towards governing Ireland upon the principles upon which alone she could now be governed’ (ib. 3rd ser. lix. 290–3). On 23 March 1843 he moved for the appointment of a select committee to inquire into the manner in which the act for the relief of the poor in Ireland (1 & 2 Vict. c. 56) had been carried into operation, but was defeated by a majority of eighty-five (Parl. Debates, 3rd ser. lxvii. 1347–69, 1405). On 30 May he opposed the second reading of the Arms Bill, and threatened ‘to divide not only on every stage of the bill, but upon every clause’ (ib. 3rd ser. lxix. 1118–20). On the removal of O'Connell and other prominent repealers from the list of magistrates by the Irish lord chancellor, O'Brien resigned his seat on the bench as a protest against such an arbitrary act. He was, however, reappointed a justice of the peace in 1846 at the special request of the magistrates of Limerick (Duffy, Four Years of Irish History, 1883, pp. 331–2). Still an avowed opponent to repeal, O'Brien, on 4 July 1843, as a final effort to obtain justice for his country, moved that the house should take into consideration ‘the causes of the discontent at present prevailing in Ireland, with a view to the redress of grievances and to the establishment of a system of just and impartial government in that part of the United Kingdom.’ In a long and forcible speech, O'Brien made a full and temperate statement of the Irish claims. While arraigning ‘the British government and the British parliament for having misgoverned’ Ireland, he confessed that he began to doubt whether ‘the abstract opinions which I have formed in favour of an union, such as seems never about to be realised, are consistent with the duty which I owe to the country possessing the first claim upon my devotion’ (Parl. Debates, 3rd ser. lxx. 630–77). O'Brien's motion, though supported by ‘young England,’ was rejected after five nights' debate by a majority of seventy-nine.
Despairing of obtaining relief from parliament, and incensed at the prosecution of O'Connell, O'Brien formally joined the Repeal Association on 20 Oct. 1843, and ‘immediately became by common consent the second man in the movement’ (Duffy, Thomas Davis, 1890, p. 188). During O'Connell's confinement in Richmond penitentiary the leadership of the association was entrusted to O'Brien, who vowed not to taste wine or any intoxicating liquor until the union was repealed (Duffy, Young Ireland, 1880, p. 481). In the federal controversy O'Brien avowed his preference for repeal ‘as more easily attainable, and more useful when attained, than any federal constitution which could be devised’ (ib. p. 592). Though he endeavoured to maintain a complete neutrality between the two sections of the Irish party, he pronounced in favour of mixed education, in spite of O'Connell's denunciations of the ‘godless colleges.’ He also opposed O'Connell in the matter of the whig alliance, declaring that his motto was ‘Repeal and no compromise.’ In the spring of 1846 O'Brien appears to have made some approaches to Lord George Bentinck, who assured him that he would cordially assent to a temporary suspension of the corn laws during the Irish famine if desired by the Irish members (Parl. Debates, 3rd ser. lxxxv. 980–92; see D'Israeli, Lord George Bentinck, a Political Biography, 1861, pp. 130–44). In consequence of his refusal to serve on a railway committee of which he had been appointed a member, a motion declaring O'Brien ‘guilty of a contempt of this house’ was carried by 133 to 13 votes on 28 April 1846 (Parl. Debates, 3rd ser. lxxxv. 1152–92), and on the 30th he was committed to the custody of the serjeant-at-arms (ib. 3rd ser. lxxxv. 1192–8, 1290–5, 1300, 1351–2). While in custody
