Thomas Kyd wrote in May 1593 that Marlowe would persuade men of quality to go to the King of Scots, where Kyd had heard Matthew Roydon had gone, and where Marlowe, when Kyd saw him last, said he intended to go. After his “death,” might Marlowe have gone to Scotland in order to covertly support English government policy?
What was happening in Scotland, a country of constant concern to England because it offered backdoor access for English enemies?
Scottish Protestant Kirk factions and pro-Vatican forces were vying for influence over Scotland’s King James VI. When the Catholic Earl of Huntly killed the Protestant Earl of Moray in 1592 and James refused to punish Huntly for it, the Kirk decided to back the man Moray had supported, Francis Stewart, 5th Earl of Bothwell. But James hated Bothwell, and he talked Parliament into declaring him an outlaw and ratifying the seizure of his estates. In response, Bothwell and his followers attacked James’ palace with a battering ram, hoping to take the king into custody. Unable to break down the door after a six-hour siege, and hearing that defenders were on the way, Bothwell fled.
During the final days of December, a carrier was found in possession of the “Spanish Blanks.” These were Spain-bound blank letters containing the signature and seals of Catholic earls of Scotland that were to be filled in and employed as proclamations in support of Spain’s invasion of Scotland and subsequently England, once negotiations with Spain were complete. The discovery of the Spanish Blanks, plus subsequent confessions, proved that Jesuits were actively seeking Queen Elizabeth’s overthrow. 
Queen Elizabeth opted to blatantly support the Earl of Bothwell, which angered King James. The English master spy Robert Poley, who was with Marlowe the day he supposedly died in Deptford, spent more than two months between December 1592 and March 1593 “riding sundry places” in Scotland.  Lord Burghley was hopeful that the Earl of Bothwell might be employed to goad King James into action against the Catholics, and corresponded with Scotland-based English agent Henry Locke in February 1593, instructing him to ask Bothwell what services he was prepared to render. 
Still obsessed with Bothwell, James convinced Parliament to declare Bothwell a traitor. Elizabeth sent a message suggesting that Bothwell should be pardoned, to which James exploded that he would rather be a slave in the Turk’s galleys than forgive him. Parliament formally attainted the Earl of Bothwell on July 21. In doing so, it nullified his civil rights, including the right to own property or use a title of nobility.
Tensions culminated in the extraordinary events of July 24, 1593 at Holyrood Palace in Edinburg. This is how Otto J. Scott described them:
[James] was sitting in his closet at Holyrood at 8 A.M. Hearing noises, he emerged with his pants in his hands, still in his nightgown, to see the earl of Bothwell coming toward him with a naked sword.
Behind Bothwell were the figures of the laird of Spott, William Leslie, and John Colville. The trio were carrying large pistols. The earl, looming before the astonished king, took a tone somewhere between contempt and a horrid jolliness.
“Loe, my good bairn,” he said. “Ye have given out that I sought your life. Now, it is in my hands. What a wrong you have done me!”
James, white as his gown, ran toward Queen Anne’s door and hammered on it, but it remained closed and still. Bothwell, moving easily, caught him by his nightgown and turned him around. James, flattened against the door, stammered.
“What do you mean?” he asked. “Are you after my life? You can get it, but you will not get my soul!”
Bothwell, however, sank gracefully to his knees and offered the sword. He was loyal; the king could strike him if he did not believe it. Matters had gone far enough; it was not necessary to frighten the king to death. 
Bothwell’s grace caused a temporary repairing of his relationship with the king, over which James announced himself delighted, although James suspected Elizabeth’s hand behind Bothwell’s actions. He pardoned Bothwell and restored his estates.
How did Bothwell go from attacking the King’s palace with a battering ram the previous year, to being let in by accomplices and offering his unsheathed sword to James, telling him to strike if James doubted his loyalty? It sounds like something out of a play.
Wait a minute, it is out of a play: Shakespeare’s Richard III, which had not been performed by July 1593, according to Giles Fletcher the Elder.  In the drama, Richard Gloucester has murdered Lady Anne’s father, Henry VI, and her husband, Edward IV. She seethes with hatred toward him, yet despite this, Richard plots to wed her. After she rails and spits on him, he kneels, offers Lady Anne his sword, and tells her to kill him (I.ii.161-73). The gesture is the first step in winning her over and she does marry him, to her later regret.
Might the episode between King James and Bothwell have been a dramatic scene staged by England’s greatest playwright in order to further the interests of England? Plans to involve Marlowe in the affairs of Scotland would have provided Lord Burghley and others with the motivation to help Marlowe out of his jam with the Archbishop of Canterbury, even if it involved staging Marlowe’s “death.”
I propose that English agent Christopher Marlowe, who said he had plans to go to Scotland, coached Bothwell behind the scenes into making the uncharacteristically magnanimous gesture of offering his sword to the king and telling the king to strike if he pleased, and that Marlowe knew about Richard III’s similar scene between Richard and Lady Anne because he wrote it.
Indeed, between June 2, 1593, the day after the inquest into Marlowe’s “death,” and June 8, when intelligencer Robert Poley delivered letters to the Queen, Poley may have been escorting Marlowe to Scotland. These letters “of great importance” really ought to have been delivered directly to Queen Elizabeth upon Poley’s arrival in England from the Netherlands just before Marlowe’s inquest. Apparently he was doing something else that took precedence.
Thomas of Woodstock
Perhaps the writing project Marlowe was working on prior to his May, 1593 “death” was the anonymous manuscript play known as Thomas of Woodstock, a precursor to Richard II. Michael Egan published a four-tome set devoted to demonstrating that William Shakespeare wrote the drama. The play appeared to parody the incident of the Spanish Blanks, knowledge of which was public by January, 1593.
It is historically accurate that Richard II forced rich Englishmen to sign blank charters which the king could fill in with an amount of his choice in order boost his income, although this occurred ten years after Chief Justice Robert Tresilian’s execution in 1388 instead of beforehand, as in the play. As always, though, a playwright must pick and choose what to include in a history play, and the inclusion of the blank charters in Thomas of Woodstock was likely no mere coincidence:
King Richard. Thou toldst me, kind Tresilian, thou’dst devised
Blank charters, to fill up our treasury,
Opening the chests of hoarding cormorants
That laugh to see their kingly sovereign lack.
Let’s know the means we may applaud thy wit.
Tresilian. See here, my lord, only with parchment, innocent sheepskins. Yet see here’s no fraud, no clause, no deceit in the writing.
All. Why, there’s nothing writ!
Tresilian. There’s the trick on’t.
These black charters shall be forthwith sent
To every shrieve through all the shires on England,
With charge to call before them presently
All landed men, freeholders, farmers, graziers,
Or any else that have ability.
Then in your highness’ name they shall be charged
To set their names and forthwith seal these blanks;
That done, these shall return to court again,
But cartloads of money soon shall follow them.
Scroop. Excellent Tresilian!
Bushy. Noble Lord Chief Justice! 
The subject of the Spanish Blanks would have been topical in the spring of 1593. As an intelligencer with an interest in history, Marlowe would have been knowledgeable about current events in Scotland and able to make the connection between them and the goings on in the court of young Richard II. Marlowe having to flee England before the play was polished might account for its fine but not timeless quality, as well as why it was never published. 
Thomas of Woodstock as it has come down to us involves at least one other hand of someone who made revisions after 1600, adding contractions and oaths not found in 16th century works. Its manuscript is missing its final page or pages.