The search, it is fairly certain, brought to light nothing of a seditious or politically objectionable nature. But that did not save Kyd; his arrest had evidently been determined on by the Government. Searching his chamber, the officers discovered something else, something which furnished them with an excuse for arresting him and conveying him to Bridewell prison. This discovery consisted of three sheets of paper (written in a neat and easily legible hand) which the officers regarded, or pretended to regard, as a treatise on atheism.[6] The possession of such a document was in those days a dangerous matter, certainly far more dangerous than to have in one's possession literature attacking the French and Dutch residents of the city. The Privy Council frowned on atheism, even though they often dared not prosecute those they suspected to be guilty of the offence.

Fortunately these three sheets of paper have been preserved. The back of the third sheet bears the following inscription, in all probability in the hand of the officer making the arrest: "12 May 1593/ Vile hereticall Conceiptes/ denyinge the deity of Jhesus/ Christe or Savior fownd/ emongest the paprs of Thos/Kydd prisoner/."

In connection with this almost lawless arrest three significant facts stand out in bold relief:

1. The alleged treatise is, as I have tried to prove in my book on the Moore manuscript,[7] in Kyd's handwriting.

2. Kyd, though he must have been aware of the seriousness of the charge against him and of the danger he was in, refrained from entering a general denial in his defence. He could have maintained—correctly, as Professor Boas informs us—that the papers were not atheistical; that they were, in fact, "a defence of Theistic or Unitarian doctrines," and that they were (as Professor W.D. Briggs[8] has recently shown) only a transcript of material contained in John Proctor's book, The Fall of the Late Arrian (published in 1549). Instead of making this perfectly obvious plea, Kyd, apparently accepting the officer's characterization of the documents, chose a most remarkable line of defence. He asserted that these papers were not his, that the alleged disputation had, as a matter of fact, emanated from Christopher Marlowe. Thereupon the officer making the arrest added the following words to the previously quoted notation on the back of the third page: "wch [papers] he [Kyd] affirmethe That he/ had ffrom Marlowe."[9] That these words were added some time, probably a few days, after Kyd's arrest, may be inferred from the following circumstances: the ink in which they were written is not that of the rest of the memorandum (Boas), and the writing, though in the same hand, is slightly different (larger and freer).

3 The cautious wording of the allegation regarding Marlowe must be noted. Kyd was careful not to say that Marlowe had written the alleged atheistical treatise. Had he done so, Marlowe would unquestionably have been able to prove that the penmanship was not his. Kyd did not say that the opinions expressed in the document were Marlowe's, nor even that the papers were Marlowe's property. All he said was that he "had" them from Marlowe. From all of which it is fairly certain that when these memoranda were written, Marlowe was still alive and that Kyd thought it best to be cautious in attacking his former associate.

How he came into possession of the dangerous document, Kyd explained subsequently (the date is not known) to the President of the Star Chamber, Sir John Puckering, in a letter in which he pleaded for his Lordship's assistance in recovering his former position in the service of Ferdinando Stanley, Lord Strange,[10] and in which he tried to minimize his relations with the atheist Marlowe. He wrote to his Lordship: "When I was first suspected for that libell that concern'd the state, amongst those waste and idle papers (wch I carde not for) & wch vnaskt I did deliuer vp, were founde some fragments of a disputation, toching that opinion [atheism], affirmd by Marlowe to be his, and shufled with some of myne (vnknown to me) by some occasion of or wrytinge in one chamber twoe yeares synce."[11]

It will be noticed that, even though Marlowe was dead when this letter was written, Kyd did not say that the alleged atheistical papers were in Marlowe's handwriting. He contented himself with vehemently reiterating his innocence and with alleging that Marlowe, who (he said) made no secret of his atheism, had shared his room with him and that in this way their papers might have got mixed. How long they had shared one chamber he did not say; but it is clear that he was trying to give the impression that it was for only a very short time ("some occasion"), even though that makes it extremely improbable that any of Marlowe's papers should have accidentally got mixed with his without either one having noticed it, and even more improbable that he would not have returned them to his associate or thrown them out.