Johnson took an active part in the defence of Basing House, becoming lieutenant-colonel to Sir Marmaduke Rawdon, the governor, and on 14 September 1644, during a skirmish with a detachment of Sir William Waller's troops under Colonel Richard Norton, he received a shot in the shoulder, "whereby contracting a feaver, he died a fortnight after" (Siege of Basing Castle, 1644).

This, the first local catalogue of plants published in England, was entitled "Iter Plantarum Investigationis ergo susceptum a decem Sociis in Agrum Cantianum, anno Dom.

1629, Julii 13" (London, 1629), and an appendix of three pages is headed "Ericetum Hamstedianum seu Plantarum ibi crescentium observatio habita anno eodem 1 Augusti."

Johnson seems (Herball, p. 450) to have been in Kent in 1626, and to have revisited both that county and Hampstead Heath, as in 1632 he published an enlarged edition of both lists.

[3] In 1634 Johnson published Mercurius Botanicus; sive Plantarum gratia suscepti itineris, anno 1634, descriptio, a description, in seventy-eight pages, of a twelve-day tour to Oxford, Bath, Bristol, Southampton, and the Isle of Wight, with English and Latin names of the plants observed.

The minor botanical works of Johnson, which became very scarce, were collected and edited by T. S. Ralph in 1847, under the title of Opuscula omnia botanica Thomæ Johnsoni.