The Murder of Christopher Marlowe
Why Was He Murdered? Theory Three
Which brings us to a third explanation. Marlowe was a known member of a heretical group led by the famous Sir Walter Raleigh, an important Elizabethan figure who was alternately in and out of favor with the queen. The Raleigh group was opposed by a rival group that also sought the favor of Elizabeth I, led by the Earl of Essex. In one way or another, Marlowe, in his role as a spy, or possibly because of his dangerous atheistic talk, had to be silenced. The question remains whether Raleigh needed Marlowe out of the way, or Essex needed, for some reason, to silence Marlowe. Key to this question is the relationship of Thomas Walsingham to these two rival factions.
Walsingham, no longer under the protection of his recently deceased relative, Sir Francis Walsingham, was involved in the "study group" led by Raleigh, and, as such, could be painted with the same brush of heresy. It wasn't simply the heretical views of the Raleigh faction, but the fact that such heresy was also a threat to the authority of the queen. It was a fatal combination of disbelief and treason. The new spymaster, Sir Robert Cecil, was as dogged as his predecessor, and would have little regard for Thomas Walsingham's position.
It is curious that all three of the men present with Marlowe at Deptford were nefarious characters. All three, along with Marlowe, had been spies (and, in the case of Poley, would continue as an active agent). It is even more remarkable to accept the strange fact that Poley and Skeres stood by while the struggle between Frizer and Marlowe was going on. One might assume that Frizer "drew the short straw" and was the designated assassin, while his two colleagues were available should Frizer encounter some difficulty with their intended victim.