In amongst Toland's papers upon his death at Putney in 1722 was A Secret History of the South Sea Scheme, which Pierre Des Maizeaux admitted was heavily annotated in Toland's hand. This offered an initiate's rendition of the trauma, arguing against the common understanding that it was a concatenation of the directors’ mismanagement and the foolishness of the crowd that had brought down the company. Rather, as it synopsized its own contents, the thesis it laid out was that:

This treatment of the South Sea Scheme as the design of three wicked figures was sustained right through the crash and the loss by one director of £200,000.

A secret history such as this at once appealed to Toland's desire to seek out hidden motivations and to be part of an initiated few who understood the true actions of the powerful. As Michael McKeon has observed ‘The aim of allegorical secret history is both to conceal and reveal the actual particularity of public personages’. Yet, it also fed into Toland's self-defence, for while he had lost money in the frenzy, he had only invested on the advice of Sir Theodore Janssen – a wealthy Tory who had been a founding figure in the Bank of England and was also a director of the South Sea Company – and a man whose reputation the pamphlet was at pains to sustain.

Toland had a vested interest in this matter for he had lost what little monies he had earned over his career in the South Sea Bubble, along with, to his embarrassment, credit he had been extended by his patron, Robert Molesworth.