The occasion for this work was a disputation in which Abbot had been involved, with a Marian Father Paul Spence who was being held prisoner in Worcester Castle. "Antichristi Demonstratio" [A Demonstration of Antichrist] (1603), was against Bellarmine once more. It was admired by the new king James I, who ordered material from his own "Paraphrase on the Apocalypse" to be printed with it in a second edition of 1608. Abbot was concerned to refute Bellarmine's reading of the "Book of Revelation" as literal and innovative (by comparison with the tradition of Nicholas of Lyra on Revelation 13), and to attack what would be identified later as the futurist approach in the tradition of Francisco Ribera. Abbot's own reading was typically historicist and concerned to argue for the Pope as Antichrist. His "A Defence of the Reformed Catholic of Mr. William Perkins" (3 vols, 1606–1609), won Abbot royal favour and a promise of preferment. It was an intervention defending the late William Perkins from an attack by the Catholic priest William Bishop. The work responded to a royal commission and prompting from Richard Bancroft, and in the first part covered the ground of the Gunpowder Plot. Abbot in the main argument of the "Defence" indicates his Puritan sympathies by deriving the true tradition of the Early Christian Church through the Albigensians, Lollards, Huguenots, and contemporary Calvinists. In the concluding part Abbot drew "the true ancient Roman Catholike" as he himself conceived the character. He dedicated the book to Henry Frederick, Prince of Wales, who promised that Abbot should not be forgotten. Abbot returned to the theme of the Plot in his "Antilogia" (1613), defending the condemnation of Henry Garnet. It used both state papers and scurrility; taking the form of a reply to the Jesuit Eudæmon Joannes, it was later considered by David Jardine to be the major historical work of its period on the Plot. A course of anti-Catholic lectures, read in his college, was published after his death aa "On the King's Supremacy". He wrote several commentaries on the scriptures which were not printed; among these is a Latin commentary on the "Epistle to the Romans", in four volumes folio. Abbot's manuscripts passed to the Bodleian Library by his grandson.