Interpretations of its underlying substance have differed: one question to the fore was the allegiance of recusants to the English crown, but it is now argued that internal church matters were central.
The Jesuits saw England as a missionary field, almost a clean slate, while many of the secular clergy saw their church's survival as a continuation of the institutions of the past.
Enrico Caetani had taken on the role of Cardinal Protector, given that the obvious successor to Allen in terms of involvement in the English mission, Robert Parsons, was not broadly acceptable.
The archpriest was to have authority over all secular clergy in England, and George Blackwell was chosen: he was close to the Jesuits, and his letter of appointment included instructions to co-operate with them.
[9] As framed by Thomas Graves Law, the controversy turned on Blackwell's relationship to the Jesuits as laid down by Caetani, and this was the central thrust of the appeal of 1600.
Relations between the two factions of seminary priests then improved; though there was an attempt to make out the fine print of the brief to disadvantage three appellant clergy (Bluet, Watson and William Clark).
Seeing a chance to divide the Catholics, Elizabeth initially welcomed these approaches, and her government gave some of the Appellants access to printers during the pamphlet war.
However, in 1602, disappointed at the Pope's settlement of the dispute, Elizabeth issued a proclamation accusing the Appellants of disloyalty, offering them mercy only if they gave themselves up and signed a "protestation of allegiance".
[17] Francis Barnaby was another appellant contact of Bancroft's, who communicated for him with Christopher Bagshaw, in Paris, and had worked with William Clark in writing a 1603 pamphlet against the English Jesuits.