Both Rev. Hunter and Rev. Munro continued to minister to the “faithful remnant” of Episcopalians, first in a meeting house at St Ninians in 1694, with Rev. Hunter as incumbent. This was suppressed under the anti-Episcopalian penal laws in 1696. Rev. Hunter was forced to leave Stirling and retired to Edinburgh for the time being. Rev. Munro preached a final sermon on the aptly-chosen text, “Finally, brethren, farewell. Be perfect, be of good comfort, be of one mind, live in peace; and the God of love and peace shall be with you” (2 Corinthians ). A second meeting house opened in St Ninians with Rev. Robert Lockhart as presbyter, but this was suppressed in May 1698. A third meeting house opened in August 1703, with Rev. Adam Peacock as incumbent, but it was closed almost immediately. These meeting houses operated illegally and were closed down when detected by the authorities. Thereafter Stirling’s Episcopalians worshipped clandestinely, with Rev. Hunter back as incumbent until he was imprisoned in 1708. The Toleration Act of 1712 gave some respite, making Episcopal ministry legal provided the clergy prayed for queen Anne. Congregations who accepted these terms were called “Qualified Chapels”, most of which were established after 1745. However, Qualified Chapels were not recognised by the Scottish bishops, who remained ‘non-jurors’, that is, people who would not swear an oath of allegiance to queen Anne or to the Hanoverian succession. ‘Non-jurors’ were permitted to worship, but only in private houses and only by using the English Prayer Book. A Qualified Chapel did arise in Stirling, but the date of its foundation is unknown. Rev. Hunter returned to his charge as a ‘non-juror’.
Stirling was surrounded by the homes and estates of Jacobite families, notably the Murrays of Polmaise, the Setons of Touch, the Steuarts of Allanton, the Abercrombys of Airthrey, the Moirs of Leckie, the Grahams and Dunmores of Airth. The Stirlings of Keir and Kippendavie were also sympathetic to the cause. These families gave their support to the next few incumbents, the first of whom was Rev. Walter Stirling, who arrived in 1713 and continued in office until around 1727. It is unclear whether this support was given openly or covertly.
Many Episcopalians sided with the Jacobites in the disastrous rising of 1715 and this led to the Penal Act of 1719, whereby no Episcopal priest could minister to more than nine people at a time, in addition to his own family, unless he took an oath renouncing the exiled Stuarts and promising to pray for George I. This also led to the final removal of nearly all Episcopal priests still in possession of parish churches, most of whom were in the Highlands and north-east Scotland. During this period, it is likely that the congregation met in private houses, perhaps belonging to the sympathetic landowning families.
Around 1727, Rev. Stirling was succeeded by Rev. Ninian Niving, who opened a meeting house in Torbrex around 1738. Rev. Niving was therefore incumbent at the time of the rising of 1745, which ended even more disastrously than that of 30 years earlier. Again, many Episcopalians supported the Jacobites. This led to the imposition of harsher rules under the Toleration Act of 1746 and Penal Act of 1748. Priests who did not swear allegiance to George II, pray for him by name and register their Letters of Orders were forbidden to minister to more than four people (“the prescribed four”) at any one time. The penalty for a first offence was imprisonment for six months, thereafter the penalty was transportation to the West Indies plantations for life. Penalties for lay people worshipping at Episcopalian services included being prevented from holding any public office, deprivation of the right to vote and being barred from admission to the universities and colleges. Further persecution followed quickly – no clergyman ordained by a Scottish bishop could “qualify” to conduct ordinary and open worship. In the wake of the failed 1745 rising and imposition of the penal legislation, some Episcopalians, especially landowners and merchants, decided that they no longer wished to be ‘non-jurors’, people who would not swear allegiance to the Hanoverian monarch, and supported Qualified Chapels. These were independent congregations, not recognised by the Scottish bishops, presided over by English or Irish priests who accepted the Hanoverian succession and retained an Episcopalian style of liturgical worship using the English Prayer Book. A qualified chapel was formed in Stirling, but nothing appears to be known about it beyond the fact that it came back into the Scottish Episcopal Church in 1804.
As Rev. Niving would thus have been banned from conducting public worship, the meeting house in Torbrex was almost certainly his own home, possibly made available to him by a sympathetic local landowner. The law on “the prescribed four” was evaded in Stirling, as elsewhere, by dividing large rooms into small sections separated by partitions which contained openings through which the minister’s voice could be heard by the whole congregation. No more that four people were in each partitioned area.
Rev. Niving struggled on under the penal laws until 1763, when he was succeeded by his son-in-law, Rev. George Cheyne. The congregation then moved to two houses in the OldTown. One was in Spittal Street, a house with a private staircase once known as Glengarry Lodge, and the other was in Broad Street, on the north side, now bearing on its restored frontage the motto Nisi Dominus Frustra (shorthand for Psalm 127, verse 1: nisi Dominus custodierit civitatem frustra vigilavit qui custodit - unless the Lord guards the city, the guard keeps watch in vain). The congregations continued to meet in these houses after Rev. Cheyne handed over to his son, Rev. Hugh James Cheyne in 1781.
As the country began to settle down under its Hanoverian monarchy, feelings ran less high and fear and suspicion diminished. This is shown in the appointment of the next minister, Rev. George Gleig. Born near Stonehaven in 1753, Gleig came of an ardent Jacobite family, but early in life came to terms with the new regime. After a brilliant career at King’s College, Aberdeen, and occupying the charges of Crail and Pittenweem, he succeeded the second Rev. Cheyne in 1787. Rev. Gleig continued to minister in the meeting houses after the passing of the Relief Act 1792, which repealed the Penal Laws. The meeting house congregations, under his leadership, “set themselves to building a church, or ‘chapel’ as it was more humbly called”. This was, for the “faithful remnant” a new beginning of freedom.