In 1586 Garnet returned to England as part of the Jesuit mission, soon succeeding Father William Weston as Jesuit superior, following the latter's capture by the English authorities. Garnet established a secret press, which lasted until late 1588, and in 1594 he interceded in the Wisbech Stirs, a dispute between secular and regular clergy. He preferred a passive approach to the problems Catholics faced in England, approving of the disclosure by Catholic priests of the existence of the 1603 Bye Plot, and exhorting English Catholics not to engage in violent rebellion.