In 1634 he published in the Netherlands two anti-Catholic Latin treatises: Elenchus Religionis Papisticae, an answer to a Catholic called Richard Short; and Flagellum Pontificis, an argument in favour of Presbyterianism.
He had Bastwick brought before the Court of High Commission, where he was convicted of a "scandalous libel", was condemned to pay a fine of £1,000 and costs, and was imprisoned in the Gatehouse Prison adjoining Westminster Abbey until he should recant.
In 1636 Bastwick published Πράξεις τῶν επισκόπων, sive Apologeticus ad Praesules Anglicanos, written in the Gatehouse against the high commission court.
The Letanie was printed by a Dutch press for John Lilburne, who had been brought to the Gatehouse in 1636 by the clothier Thomas Hewson and minister Edmund Rosier.
Lilburne was just finishing an apprenticeship with Hewson, and smuggled the text abroad, but was betrayed by his assistant in importing the Letanie, John Chilliburne, who worked for Wharton.
The Parliamentary success in the war brought by 1645 a new relationship between the Presbyterians and other Protestant groups, classified as Independents, such as the emerging Quakers and Congregationalists.
Bastwick with Prynne was a hard-liner on the Presbyterian side; Burton wanted a less harsh approach, and by then Lilburne was a very popular Independent, beginning to found the Levellers.
[5] Bastwick with Colonel Edward King arranged for Lilburne to be arrested on 19 July 1645 for words he had said against the Speaker of the House of Commons; he was in custody until October.