The bishop of Meath, Patrick Plunket (qv), granted Martin faculties for the diocese in March 1789, but the friar's pastoral activities took him into the neighbouring dioceses of Armagh and Dublin, and there are reports of his preaching as far away as Kilbride, Co. Wicklow. These travels brought him through the heartland of Defenderism, while in Drogheda he could not fail to have been affected by rising political tensions, exacerbated by the anti-Defender trials orchestrated in 1794 by the speaker of the Irish house of commons, John Foster (qv).
Martin joined the Society of United Irishmen in Easter 1797, having been sworn by two Franciscan friars, Patrick Duffy and James MacCartan. Following his political conversion he joined the Drogheda committee of the United Irishmen and was actively involved in promoting the principles of the society, in the city and beyond; in May 1798 General Lombard warned that ‘every day the public mind here about is becoming more ripe for action’ (NAI 620/39/20).
Following the outbreak of the rebellion of 1798 John Martin received a number of significant commissions from the Dublin United Irish Committee, based at Thomas St., which had assumed the functions of the directory, following the arrests at the house of Oliver Bond (qv). In his first assignment, in the early days of June, the friar was dispatched to Dunboyne, Co. Meath, and Manor Kilbride, Co. Wicklow, in order to reanimate the United Irish campaign, which had fallen into disarray following the defeat of the rebel army at the battle of Tara on 26 May 1798. On this mission, the priest encouraged the men to continue the struggle: ‘if you . . . have sworn to be faithful to one another, now that you see your houses burned is the time you are called to keep your oath’ (NAI 620/28/126).
Martin's second mission was more ambitious. The Dublin committee instructed him to ride south to Wicklow and Wexford, where the rebels still maintained a good deal of their original momentum, in a desperate attempt to coordinate an assault on Dublin, planned for 12 June. Martin set off for Arklow; en route he met with United Irish leaders, including Joseph Holt (qv), with whom he spent almost an hour discussing military plans from a vantage point above Rathfarnham, Co. Dublin. From there he rode south to Cronebane, Co. Wicklow, where he intended to liaise with the local United Irish leaders, but he was captured on 11 June by the Rathdrum yeomanry.
The friar was interrogated by Capt. John Giffard (qv) of the Dublin city militia, who described him as ‘the greatest villain in society’ (NAI 620/38/160). Under threat of execution, Giffard extracted a full confession, which contained details on the politicisation of Drogheda and the revised military plan of the United Irishmen. On the strength of this confession several arrests were made in Drogheda, but the friar's evidence appears to have been insufficient to secure convictions. Martin was lodged in Kilmainham gaol, Dublin. In March 1800 he appealed to Richard Annesley at the Custom House to intervene on his behalf, but to no avail. Finally (5 August 1801) Martin made his escape by ladder from the prison and disappeared without trace, despite a reward of fifty guineas offered for his capture.
Martin has been neglected in the historiography of the rebellion. In many respects he was not easy to accommodate in the traditional interpretations, on account of his explicit politicisation, which suited neither loyalists nor rebel apologists who were anxious to present the rebellion as a spontaneous response to oppression. Neither did his role as informer facilitate his incorporation in the legends created by Fr Patrick Kavanagh (qv) in the late nineteenth century. More recently, historians have focused on Martin because his mission illustrates two significant points in the new historiography: both the overarching military plan for the rebellion of 1798 and its United Irish inspiration and direction.