In 1690 Queen Mary was attacked with small-pox, and to the inexpressible grief of her husband, shared by the greater part of the nation, she died after a very short illness. Friendly messages had been exchanged between her and her sister, but Mary’s state was too critical to allow of her being exposed to the excitement of an interview. When the last scene was over, and the last duties paid to the beloved Queen and consort, the attempt at reconciling the Princess of Denmark and her brother-in-law was renewed, and Lord Sunderland, the Duke of Marlborough, and Sir John Som̅ers, joined to promote the wished-for result. Anne had been persuaded to write to the King, who, stunned by grief, showed little inclination to respond to her advances. Som̅ers therefore, bent on carrying out his object, made his way into the Royal presence at Kensington, where he found William absorbed in speechless grief. He waited for some time in respectful sympathy, hoping that the King would break the painful silence, but was at length compelled to take the initiative.

With the gentle delicacy that characterised him, the Lord Keeper broached the subject, pointing out how essential it was, on public as well as private grounds, that the enmity between his Majesty and his wife’s sister should cease. ‘Do as you will,’ replied the unhappy widower, ‘I can think of no business.’ An interview was accordingly arranged. Anne was graciously received, apartments assigned her in St. James’s Palace, and due honour paid her as heir-presumptive to the Crown. William once more pressed a Peerage on Sir John (through his friend, now Duke of Shrewsbury), but it was again declined. He was placed virtually at the head of the Regency (the Archbishop of Canterbury presiding only in name), when the King again left England for a foreign campaign.

He took a prominent part in the great measure for the reformation of the coinage, and drew up and strongly advocated a plan by which clipping money could be prevented; but this was not carried into effect. Lord Macaulay praises him highly for the appointments he made of such eminent men as Sir Isaac Newton and John Locke, for the respective posts of Warden of the Mint and a Lordship of Trade.

In 1697 Sir John resigned the Seals, only to have them returned to him, with the title of Lord Chancellor and Baron Som̅ers of Evesham, county Worcester, as also grants of the manors of Reigate and Howleigh in Surrey, with a yearly income to enable him to keep up the same. On the retirement of Lord Godolphin, the Ministry became wholly Whig,—Montagu, Russell, Som̅ers, and Wharton forming ‘the Junto.’ In the same year the Peace of Ryswick was signed, by which France made great concessions, and acknowledged William as King of England, and Anne as his successor, a circumstance which gave rise to much rejoicing. But serious differences took place between the King and his Parliament, which required the disbanding of the troops that had done such good service in foreign campaigns. The most stormy discussions ensued, and the press, in all the wild ardour of recent emancipation, thundered with controversy. To Lord Som̅ers was attributed (indeed Macaulay speaks of the authorship as a certainty) a treatise, called ‘The Balancing Letter,’ which made a great noise at the time, weighing, as it did, the arguments for and against the momentous question, but undoubtedly leaning towards the advisability of maintaining a small standing army. In spite of William’s vehement opposition, he found himself compelled to ship off his beloved Dutch Guards, and to diminish the English forces.

Until this time the life of John Som̅ers had been uninterrupted in its prosperity and advancement; but a change in his fortunes was now impending. Henceforward he had both public and private trials to encounter, added to which, his health had become much impaired. In July 1698, Parliament being dissolved, and the King gone to Holland, Lord Som̅ers gladly availed himself of the opportunity to recruit his bodily powers, by drinking the waters in the pleasant retirement of Tunbridge Wells. The question of the Spanish succession (Charles II., king of that country, being at the time in a dying state) belongs rather to the political history of Europe than to the biography of an individual, yet Lord Som̅ers was so intimately connected with the so-called ‘Tradition Treaties,’ that we cannot altogether keep silence on the matter. Before the King’s departure for Holland, William had already consulted Som̅ers on the subject, and, on arriving at the Loo, he wrote, authorising him to consult with any of his colleagues, on whose discretion and secrecy he could rely, and asking for opinions on the arrangement proposed, which his Majesty detailed at full length. Now such a treaty could not be concluded without the appendage of the Great Seal and the signature of one Secretary of State. The Lord Chancellor was therefore directed to send full powers to the Loo, sealed, but with blanks left for the names of the Plenipotentiaries; and it was strongly urged that the clerks whose duty it was to draw up the documents should be kept in profound ignorance of the subject, and the importance of the work they were performing. The Royal missive found ‘Som̅ers at a distance from his political friends, his delicate frame enfeebled by the labours and vigils of many months, and his aching head giddy with the first draughts of the chalybeate spring.’ But he lost no time, and communicated promptly with all the leading statesmen, who agreed with the King in wishing to see the question of the Spanish succession settled without delay. Som̅ers, however, delicately hinted to his master that he and his colleagues had misgivings on many points of the treaty, although the Royal wishes had been complied with.

The powers were sent off, the enjoined secrecy observed, the blanks left for the names of two Commissioners, who, the Lord Chancellor suggested, should be English, either by birth or naturalisation, and consequently responsible to Parliament.

A second Partition Treaty was shortly afterwards drawn up and signed, with fresh clauses and allotments to the different European powers, with the same secrecy; and when the terms of these treaties became known in England, a great outcry was raised against the Whigs, and strenuous efforts made to overthrow the Administration. The Lord Chancellor, in particular, became the mark for attacks of different kinds, such as his misconduct in the appointment and dismissal of magistrates, while a novel charge for the dignitary of the Woolsack was adduced against John Lord Som̅ers, namely that of piracy on the high seas,—not in person, indeed, but by proxy. Thus it came about: he, in common with other Ministers, had subscribed a sum of several hundreds towards the fitting out of a ship called The Adventure Galley, for the purpose of ridding the Indian seas of pirates. The command was given to Captain William Kid, a naval officer, who had hitherto borne a high character for honour as well as courage.

As may easily be believed, Lord Som̅ers knew nothing of the matter further than that he thought it became the post he occupied to assist in such a public service; and a grant was made to all the undertakers of the scheme that they should become possessed of any booty taken from the pirates by their ship. Captain Kid was armed with full powers to sink, burn, and destroy the pirates, but on breathing the air of the buccaneering seas, he turned pirate himself, and became a dangerous foe to honest traders of all nations, till, after a sharp encounter with an English frigate, he was taken, and brought home in irons. A motion was now brought forward by his (Som̅ers’s) political adversaries, that the Lord Chancellor should be made responsible for all the outrages committed by Kid, with whom, they affirmed, he had intended to go shares for the purpose of swelling his own coffers,—‘Such black constructions,’ says Burnet, ‘are men apt to put on the actions of those whom they intend to disgrace.’ The charge, being preposterous, was rejected by a large majority.

A Bill was now brought in to resume the Irish forfeited estates, which the King had bestowed on his Dutch favourites, and Lord Som̅ers incurred both the Royal displeasure and that of the Opposition in Parliament for his absence during the debates, although he pleaded the excuse of bad health. William expected assistance from the Chancellor in opposing this measure, but the public opinion was so strong that Som̅ers did not consider it advisable to support his Majesty. His enemies had now become persistent in their attacks; and a motion was made in the House of Commons to the effect that ‘the King should be advised to remove the present Lord Chancellor from his councils for ever,’ in common with other leading Ministers.

He had been absent from his duties for some time, in consequence of failing health, in spite of which the Opposition did all in their power to induce him to coalesce in the formation of a new Government; and in answering the overtures made him by Lord Sunderland, Som̅ers replied that he considered such a step would be inconsistent with honour.