Ireland was then in a rebellious and discontented condition, and it was difficult for the English government to decide either on a definite course of policy with regard to it, or on a leader by whom that policy might be carried out. A violent quarrel took place between the queen and Essex, who for some months retired from court and refused to be reconciled. At last he came forth from his seclusion, and it was soon understood that he was in person to undertake the subjugation of the rebels in Ireland, with a larger force than had ever before been sent into that country. Into the obscure details of this unhappy campaign it is unnecessary to enter; one fact stands out clearly, that Essex endeavoured to carry out a treasonable design. His jealousy and ill-temper had been so roused that the only course open to him seemed to be the obtaining a powerful military force, the possession of which would compel the queen to reinstate him in her favour. Whether or not this plan was in contemplation before he undertook the Irish expedition is not evident, though even outsiders at that time entertained some suspicions, but there can be no doubt of the treasonable character of the negotiations carried on in Ireland. His plans, probably not very definite, were disturbed by an imperative message from the queen, ordering him not to return to England without her permission.

He at once set off, and, trusting apparently to her affection for him, presented himself suddenly before her. He was, for the moment, received kindly, but was soon afterwards ordered to keep his chamber, and was then given into the custody of the lord keeper at York House, where he remained till March 1600. His great popularity, and the general ignorance of the reasons for his imprisonment, stirred up a strong feeling against the queen, who was reported to be influenced by Bacon, and such indignation was raised against the latter that his friends feared his life would be in danger. It was at last felt necessary that the queen should in some way vindicate her proceedings, and this she at first did, contrary to Bacon's advice, by a declaration from the Star Chamber. This, however, gave little or no satisfaction, and it was found expedient to do what Bacon had always recommended, to have a fair trial, yet not one in which the sentence must needs be damaging to the earl. The trial accordingly took place before a body of her majesty's councillors, and Bacon had a subordinate and unimportant part in the accusation.

Essex does not seem to have been at all hurt by his action in this matter, and shortly after his release they were again on friendly terms, Bacon drawing up letters as if to or from the earl with the design of having them brought before the queen. But Bacon did not know the true character of the transactions in which Essex had been engaged. The latter had been released from all custody in August, but in the meantime he had been busily engaged in treasonable correspondence with James of Scotland, and was counting on the Irish army under his ally, Charles Blount, Baron Mountjoy (afterwards earl of Devonshire), the new deputy. But Mountjoy had apparently come to see how useless the attempt would be to force upon the queen a settlement of the succession and declined to go farther in the matter. Essex was thus thrown upon his own resources, and his anger against the queen being roused afresh by the refusal to renew his monopoly of sweet wines, he formed the desperate project of seizing her person and compelling her to dismiss from her council his enemies Raleigh, Cobham, and Cecil. As some pretext, he intended to affirm that his life was in danger from these men, who were in league with the Spaniards. The plot was forced on prematurely by the suspicions excited at court, and the rash attempt to rouse the city of London (8th of February 1601), proved a complete fiasco.

The leaders were arrested that night and thrown into prison. Although the actual rising might have appeared a mere outburst of frantic passion, the private examinations of the most prominent conspirators disclosed to the government a plot so widely spread, and involving so many of the highest in the land, that it would have been perilous to have pressed home accusations against all who might be implicated. Essex was tried along with the young earl of Southampton, and Bacon, as one of her majesty's counsel, was present on the occasion. Coke, who was principal spokesman, managed the case with great want of skill, incessantly allowing the thread of the evidence to escape, and giving the prisoners opportunity to indulge in irrelevant justifications and protestations which were not ineffectual in distracting attention from the real question at issue. On the first opportunity Bacon rose and briefly pointed out that the earl's plea of having done nothing save what was absolutely necessary to defend his life from the machinations of his enemies was weak and worthless, inasmuch as these enemies were purely imaginary; and he compared his case to that of Peisistratus, who had made use of a somewhat similar stratagem to cloak his real designs upon the city of Athens. He was thereupon interrupted by the earl, who proceeded to defend himself, by declaring that in one of the letters drawn up by Bacon, and purporting to be from the earl to Anthony Bacon, the existence of these rumours, and the dangers to be apprehended from them, had been admitted; and he continued, "If these reasons were then just and true, not counterfeit, how can it be that now my pretences are false and injurious?" To this Bacon replied, that "the letters, if they were there, would not blush to be seen for anything contained in them, and that he had spent more time in vain in studying how to make the earl a good servant to the queen than he had done in any thing else." It seems to be forgotten in the general accounts of this matter, not only that Bacon's letters bear out what he said, but that the earl's excuses were false.