Throughout his twenty-year career as the Archbishop of Canterbury, John Whitgift enjoyed the confidence of Queen Elizabeth, who nicknamed him her “little black husband.” In the spring of 1593, Whitgift was on the warpath against those he viewed as enemies of the Church of England. Puritan separatists Henry Barrow and John Greenwood were executed on April 6, 1593, and Anglican church critic John Penry on May 29. The Queen’s de facto prime minister, Lord Burghley, had rebuked Archbishop Whitgift publicly for his violent methods, and in vain did what he could to save Penry, Barrow and Greenwood from hanging.  Accused of heresy, playwright Christopher Marlowe’s well-timed “death” on May 30th kept him from being next to experience imprisonment, torture and probable execution. Yet Marlowe was different from the others: as an intelligencer, he was a valuable asset to the State.
Might Burghley, who was spymaster in 1593 and had helped get Marlowe out of jams twice in the past, have convinced the Queen to covertly help Marlowe to avoid execution, without overtly contradicting the archbishop? Might Marlowe, writing as “Shakespeare,” have signaled his displeasure with Witgift’s persecution, and with the Queen for not publicly coming to his defence, forcing him to have to pretend to die?
The Blind Beggar of Alexandria
A possible clue appears in The Blind Beggar of Alexandria, the first extant play by George Chapman, composed in 1596. George Chapman (1559/60-1634) was the son of a yeoman, and spent his early adulthood in the house of Sir Ralph Sadler, a diplomat and government administrator who was one of the richest men in England. Chapman fought abroad in Europe, and upon return, became a prolific poet, playwright and translator.
Chapman wrote a continuation of Marlowe’s Hero and Leander in 1598, and both he and Marlowe were associated with a group that Jesuit Robert Parsons called Sir Walter Ralegh’s “school of atheism,” alternatively thought of by some scholars as a Ralegh-Northumberland Circle of free thinkers.
Chapman’s comedy The Blind Beggar of Alexandria tells the story of Duke Cleanthes, who is banished from Egypt by King Ptolemy. He returns to Egypt and operates under three disguises, a blind fortune teller named Irus, a one-eyed Count Hermes, and a fully sighted Leon, a usurer. Cleanthes fools everyone, ends up marrying two sisters—alternating nights with each of them—saves Egypt from conquest, and becomes king. Like Shakespeare’s Richard II, an exiled man replaces the king who banished him, but The Blind Beggar of Alexandria carries off its plot in a comic, entertaining fashion.
Marlowe’s Hero and Leander is quoted in Chapman’s play, its most famous line--"Who ever lov'd, that lov'd not at first sight?"--is paraphrased as “None ever lov’d, but at first sight they lov’d” (Scene x.130).  The woman Count Hermes eventually weds appears above the walls and says, “With this tower I would I had a torch/ To light, like Hero, my Leander hither. Who shall be my Leander?” (Scene ii.4-6). At the end of the play, when Leon must disappear so that Duke Cleanthes can reappear, it is said that he committed suicide by casting himself from a tower into the sea, exactly the same fate as Hero in Hero and Leander.
Count Hermes gets into trouble and is advised to fly to the hills beyond the Alps (Sc. ix.17-18). This mirrors language in the Prologue to The Jew of Malta, where Machevil states that his soul flew beyond the Alps. Hermes’ response contains lines imitating Marlowe’s The Passionate Shepherd to his Love, beginning “But come, sweet love, if thou wilt come with me,/ We two will live amongst the shadowy groves,/ And we will sit like shepherds on a hill” (Scene ix.24-36).
At the end of the play, the victorious Duke Cleanthes invites everyone to court with lines cobbled together from the Tamburlaine plays: “Carousing free whole bowls of Greekish wine/ In honour of the conquest we have made,/ That at our banquet all the gods may tend” (Scene x.176-8). 
Indeed, Ennis Rees viewed Blind Beggar as a deliberate “burlesque of the Marlovian hero” with Irus, like Tamburlaine, born a shepherd’s son who, by play’s end, has become king.  Irus’ hocus pocus, said Rees, recalls Doctor Faustus, while the big-nosed usurer Leon’s avaricious antics bring to mind Barabas in The Jew of Malta. Rees failed to note Blind Beggar’s burlesque of Richard II.
Within the context of a play with so many connections to Marlowe, Queen Ægiale’s opening speech in the first scene captures our attention. Queen Ægiale’s odd name is an interesting choice, given B. N. De Luna’s interpretation that Avisa, who is called “eagle-eyed” and an “English Eagle” in the anonymous Willobie his Avisa, 1594, was Queen Elizabeth :
Queen Ægiale. Ah my Cleanthes, where art thou become?
But since I saved thy guiltless life from death,
And turn’d it only into banishment,
Forgive me, love me, pity, comfort me. (Scene i.8-11, emphasis added)
The queen says she saved Cleanthes’ guiltless life from death and turned it only into banishment. I propose that this is a clue that Elizabeth did the same for Marlowe, and that Cleanthes’ return using disguises and aliases is a clue that Marlowe returned to England, but not in true name or appearance.
An intriguing interchange occurs between Cleanthes and his servant at the end of the play:
Pego. [aside] How say you, master brother, am not I secret now?
Cleanthes. [aside] Thou art, and be so still, for not the world
Shall ever know the mad pranks I have played. (Scene x.157-9, emphasis added)
The clever Cleanthes’ lines echo with possibilities: “For not the world shall ever know the mad pranks I have played.”
Richard III, Richard II and Hamlet
Did Marlowe ever forgive, love, or pity Queen Elizabeth? Shakespeare didn’t. He did not, for example, write a eulogy upon her death. In England’s Mourning Garment, Henry Chettle berated the Bard, identified by a reference to The Rape of Lucrece, for failing to do so:
Nor doth the silver-tongued Melicert,
Drop from his honied muse one sable tear
To mourn her [Queen Elizabeth’s] death that graced his desert,
And to his lays opened her Royal ear.
Shepherd, remember our Elizabeth,
And sing her Rape, done by that Tarquin, Death. 
This is the one known allusion to a relationship between the author of the Shakespeare works and the Queen: she “graced his desert,/ And to his lays opened her Royal ear.”
Indeed, the timing of Shakespeare's changed attitude toward the monarch is noteworthy. Richard III, thought to have been penned during the winter of 1592/3, performed excellent public relations work for the Tudor family. It provided ample justification for Elizabeth's grandfather--Henry, Earl of Richmond, who became Henry VII--to kill the evil Richard III and establish the Tudor line.
A few years later, c. 1595, Shakespeare penned Richard II, about a monarch who surrounded himself with corrupt cronies. The scene where Henry of Bolingbroke--who became Henry IV--returns from exile and deposes Richard II was not printed until the fourth quarto in 1608, five years after Queen Elizabeth's death. This has caused many to think that the play's printed text was censored during her reign because it obliquely critized her. We know not why Shakspere from Stratford-upon-Avon would have changed his tune toward the monarch. If Marlowe wrote both plays, the cause could have been resentment that her failure to stand up for him to Whitgift forced him into exile after a faked death, as Richard II forced Henry of Bolingbroke into exile.
In addition, Shakespeare penned Hamlet, which contains another supporting clue.
In Hamlet, Alex Jack uncovered a juxtaposition of “wit” and “gifts,” where “wit” was printed as “will” in Hamlet’s first quarto, 1603, the only one of the three quartos printed before Archbishop John Whitgift and Queen Elizabeth died.  The Ghost of Hamlet’s father is speaking about the marriage of his brother, Claudio, to his former wife, Queen Gertrude. Here is how the passage reads in Shakespeare’s First Folio:
Ghost. Ay, that incestuous, that adulterate beast
With witchcraft of his wit, hath traitorous gifts—
O wicked wit and gifts, that have the power
So to seduce!—won to his shameful lust
The will of my most seeming virtuous queen. (F.F. p. 257; I.v.42-6)
Jack interpreted this passage in Hamlet as alluding to the relationship between the Crown and the Church, between Queen Elizabeth and the Archbishop of Canterbury--that the Archbishop had seduced the Queen into approving his harsh, violent tactics against church dissenters who failed to toe the line. 
Much Ado About Nothing
Others have found another juxtaposition of “wit” and “gift” in Much Ado About Nothing.  One of its two plots revolves around a romance between Hero and Claudio. On the eve of her wedding, Hero’s reputation is besmirched and Claudio refuses to marry her. What to do? Hero pretends to be dead until her fiancé finds out that she is innocent of the charge of infidelity leveled against her, and her good name is restored. Marlovians—those who believe Marlowe wrote the bulk of the Shakespeare canon—see a decided parallel between Hero being slandered and pretending to die, and the author of Hero and Leander, Christopher Marlowe, being slandered and pretending to die in order to avoid execution as a heretic. In advising Hero, Friar Francis says, “Come Lady, die to live” (IV.i.256).
It is true that the Bard follows his source in the action of his plot—most likely the 22nd novel of Bandello, or possibly John Harrington’s translation of its translation of Ariosto’s Orlando Furioso—but where his play differs from these sources is noteworthy.  The female protagonist, named “Fenicia” in Bandello and “Genevra” in Ariosto, is named “Hero” in Much Ado, associating her with the author of Hero and Leander, Christopher Marlowe. In Bandello there is no woman who impersonates her on the balcony, while the one who does in Ariosto is “Dalinda,” as compared to “Margaret” in Much Ado, which is abbreviated to “Mar.” in some speech designations. The bad guy is called Girondo in Bandello and Duke Polynesso in Ariosto, and in both cases, he is motivated by revenge because Fenicia/Genevra jilted him. In Much Ado, he has no motivation, and is called “Don John.”
A speech by one of the other pair of lovers in Much Ado, Beatrice, juxtaposes the words “wit” and “gift” (1600 first quarto and First Folio).She is speaking of Benedict, but several lines later it is Don John who “slanders” Hero “in his villany”:
Beatrice. Why, he is the prince’s jester: a very dull fool; only his gift is in devising impossible slanders: none but libertines delight in him; and the commendation is not in his wit, but in his villany... (II.i.144-8)
Passages quietly associate Don John with the church. Marlowe had linked “religion” with “cross,” verb, in The Massacre at Paris: “Our difference in religion might be a means to cross you in your love” (Scene 1.15-6). Since he employed “cross” to mean “to thwart or obstruct,” the religious association of “cross” is subtle. Much Ado juxtaposes “cross” with “bless,” another religious term. Don John says of his enemy Claudio, “If I can cross him any way, I bless myself every way”(II.i.70). The playwright also has Borachio and Don John repeat “cross” three times in a row for emphasis, when Borachio tells Don John he can stop Claudio’s marriage to Hero from occurring:
Borachio. Yea, my lord; but I can cross it.
Don John. Any bar, any cross, any impediment will be medicinable to me: I am sick in displeasure to him, and whatsoever comes athwart his affection ranges evenly with mine. How canst thou cross this marriage? (II.ii.3-8)
In summary, The Blind Beggar can be interpreted as providing a clue that the Queen saved Marlowe’s life by banishing him, while Hamlet’s juxtaposition of “wit” and “gifts” may indicate its playwright’s anger over the close relationship between the Church and the State. Much Ado About Nothing, which contains another wit/gift juxtaposition, perhaps dramatizes Marlowe plight under the guise of what happened to Hero: Don John (Witgift) caused him to be slandered, and he pretended to be dead.
Another possible source was Sir John Harrington’s translation of Ariosto's Orlando Furioso, Canto V. In it, Ariodant falls in love with Genevra. Her jilted lover Duke Polynesso has Genevra’s servant Dalinda appear at her mistress’ balcony, to which Polynesso ascends by ladder, to convince Ariodant of Genevra’s infidelity. There is also a version of this story in Spenser’s The Faerie Queene, Book II Canto iv, 17 fol. The man is Phedon, his lady, Claribel, the villain, Phedon’s friend Philemon, and the handmaid who appeared dressed in Claribel’s clothes in a dark bower, where Philemon wooed her, Pryne. Phedon becomes so angry that he slays Claribel. When he finds out the truth from Pryne, Phedon poisons Philemon to death. Alison Findlay, Much Ado About Nothing (New York: Palgrave Macmillan, 2011).