On 6 January 1589 he expounded this view in a sermon at Great St. Mary's, Cambridge, claiming that church government by elders is jure divino.
He claimed a right of appeal, and refusing to leave; he was in December again in custody and vainly petitioning Burghley, backed by fellows of colleges.
In 1591, Johnson discovered that the Brownist Arthur Bellot was smuggling 2,000 copies of A Plaine Refutation by Henry Barrow and John Greenwood through Flushing into England.
On the advice of Lord Burghley, Johnson seized the books and burned them – but kept a copy out of curiosity, and was converted by it to Brownism.
Johnson was arrested in October 1592, and again on 5 December, this time with Greenwood in the house of Edward Boyes, a haberdasher on Ludgate Hill.
[3] After Barrow, Greenwood and John Penry were executed in 1593, under the Seditious Words and Rumours Act of 1581, much of the congregation went into exile in the Netherlands.
In 1596 he wrote the foundational Brownist document A Trve Confession of the Faith ... vvhich vve hir Majesties Subjects, falsely called Brovvnists, doo hould tovvards God.
[3][6] In 1597, Johnson persuaded the Privy Council to release him and three other Brownists to found a Puritan Separatist colony in the Magdalen Islands off the coast of Newfoundland.
[7] Francis, his brother George, his elder Daniel Studley, and a fourth member of the church John Clarke, were passengers of the merchants Abraham and Stephen Van Hardwick, and Captain Charles Leigh of Addington.
[10] On the accession of James I, Johnson and Ainsworth visited London to deliver a petition for toleration, which was unsuccessful but which they published as An Apologie or Defence of svch trve Christians as are commonly (vnjustly) called Brovvnists.
After much discussion Johnson proposed that the 'congregationalists' should move to Leyden, joining the exile church there (a group that included at some points Robert Parker, Henry Jacob, William Ames and John Robinson).
But the compromise fell through, and Ainsworth with his congregation obtained a place for worship two doors away from the meeting-house, and moved there in December 1610.