To these opinions he adhered when Lord Falkland, with the knowledge of the king, addressed him on the subject. In the same year arose the question as to the power of parliament to nominate lords lieutenant in the absence of the king with the army. It was a matter which divided the party of progress. But Selden went with the advanced guard, and accepted a commission as deputy lieutenant under a lord lieutenant appointed by parliament.
In 1643 Waller formed a royalist plot for overpowering the city militia and dissolving the parliament. One evening he went to Selden's study, where he found him, Pierrepoint, and Whitelocke, with the intention of imparting the plot to them; but after he spoke of the project in general terms Selden and his friends so inveighed against any such thing 'as treachery and baseness, and that might be the occasion of shedding much blood, that he durst not for the awe and respect which he had for Selden and the rest communicate any of the particulars to them, but was almost disheartened himself to proceed in it.' After the discovery of the plot, and Waller's arrest, Waller was examined as to whether Selden was in any way privy to his proceedings.
In the same year Selden, with some other members of both houses, sat in the assembly of divines at Westminster. In the debates of this body (says Whitelocke) 'Mr. Selden spake admirably, and confuted divers of them in their own learning. And sometimes when they had cited a text of scripture to prove their assertion, he would tell them, "Perhaps in your little pocket-bibles with gilt leaves" (which they would often pull out and read) "the translation may be thus, but the Greek or the Hebrew signifies thus and thus," and so would totally silence them.' Selden proved a thorn in the sides of the Westminster divines, for he liked the claims of presbytery no better than those of episcopacy; and, according to Fuller (Church Hist. bk. xi. sect. ix. par. 54), he used his talents rather 'to perplex than inform' his auditors, his interests being 'to humble the jure-divinoship of presbytery.'
On 27 Oct. 1643 the House of Commons resolved that the office of clerk and keeper of the records of the Tower should be sequestered into the hands of Selden, and that he should receive the profits of the place. Proceedings of the council of state in 1650 (17 Oct. and 20 Dec.) seem to show that Selden had then ceased to derive any benefit from the office, but was willing to continue in it without reward. In April 1645 he was appointed one of twelve commoners who, together with six lords, constituted a committee to manage the admiralty. In August Selden declined the mastership of Trinity Hall, Cambridge, which he was offered by the direction of the House of Commons. In September he opposed in a speech, the substance of which has been preserved, the petition of the assembly of divines that in every presbytery the pastors and ruling elders should have the power of excommunication and of suspending from the sacrament. On 24 Feb. 1646 he spoke in favour of the abolition of the court of wards.
On 18 Jan. 1647 the house resolved that Selden should have 5,000l. 'for his damages, losses, imprisonments, and sufferings sustained and undergone by him for his services done to the Commonwealth in the parliament of Tertio Caroli.' It is doubtful whether Selden received this sum; a report was current that he 'could not out of conscience take it' (Wood, Athenæ Oxon.). His conduct in a suit relating to a Mrs. Fisher's will (S. P. C. 1631, pp. 233, 371), and in relation to the office of keeper of the records, seems to show that this report is probably true. On 23 Feb. 1649 a committee was appointed by the council of state to consider the dignity and precedence of ambassadors, and Selden and Challenor were directed to assist them.
Selden took no further part in public affairs. During the trial and execution of the king and the rise of Cromwell, Selden abstained from any expression of his views. 'The wisest way for men in these times is to say nothing' was a maxim of his, on which he seems to have rigorously acted (Table Talk, Peace).
But Selden was able to protect the cause of learning during these troubled times. He procured the delivery to the university of Cambridge of Archbishop Bancroft's library; and to the university of Oxford he rendered more important services. In 1646 the vice-chancellor appealed to him to 'relieve his declining undon mother;' and when in May 1647 an ordinance of the lords and commons was made for the visitation and reform of the university, Selden was appointed one of the committee to hear appeals from the visitors. In numerous sittings of that body Selden took an active part, and was able to temper the somewhat unfair treatment to which the university was in danger of being subjected.
In spite of the pressure of his public duties, Selden's literary work had progressed steadily. From the treasures of Sir Robert Cotton's library he had edited the six books of Eadmer [q. v.], giving an account of the courts of the first two Williams and of the first Henry. To the text he appended 'Notæ
