Various theories have been put forward as to the circumstances of his death, with suggestions that he was caught up in the power struggles of the Elizabethan secret state and that he was a heretical freethinker. After Marlowe's death Richard Baines, an informer, claimed in a note to the Privy Council that Marlowe had said that "all they that love not tobacco and boys are fools" and persuaded “men to Atheism… utterly scorning both men and his minsiters” (Steane). He was said to have proclaimed the heresy “That Saint John the Evangelist was bedfellow to Christ and leaned always in his bosom; that he used him as the sinners of Sodoma”.
Such speculation informs Anthony Burgess’ fictionalised life ‘A Dead Man in Deptford’ (1993), in which Marlowe is ‘soothed by the noise of the waterside taverns, where there was much hard drinking’ in an imagined 16th century Deptford with ‘the shipbuilders early awork. The chandlers’ shops busy. Hounds from the Queen’s kennels howled bitterly. A faint stink from the Queen’s slaughterhouse. But was not the whole land her slaughterhouse? A firmer stink from the tanneries. Inland gulls wove over the waters and crarked. Sails, sails, a wilderness of them”.
A more outlandish fictionalisation by Rosemary Laurey, ‘Walk in Moonlight’ (2000), has Marlowe as a vampire!
Now there's Fear and Loathing in Deptford by K.A. Laity, in which Marlowe meets a fairly joyous end after a night of sex and psychedelic potions: 'How I am glutted with this cheap Spanish venom. Why, why this night? What desperate enterprise brought me hither, to drink, to danger, to the damp smells of this dim hostelry? Jack is crawling through the dust, murmuring a wild soliloquy of blistering loss and betrayal. Jack, oh yes. We had begun the afternoon in his cheerless study, surrounded by the parcels and bottles of his trade, the rank stench of his potions and unguents. As usual, he was bubbling with servile enthusiasm for a new discovery, the latest translated from some book of Cornelius Agrippa. Having canvassed every quiddity thereof, he swore this would be the best yet. I remembered too well, however, the last miracle, the one that left us barking like dogs and then retching like them too'.
Give it a read at The World SF Blog (thanks to Richard S. for spotting this).