Comyn was thus Nelson's Chaplain at the time of the Battle of the Nile. At the battle the injured Nelson believed he was dying and sent for Comyn. Nelson recovered and following the victory, issued a memorandum to his fleet, "Almighty God having blessed His Majesty's arms with victory, the Admiral intends returning public thanksgiving for the same at 2 o'clock this day and he recommends every ship doing the same as soon as convenient." Reverend Comyn conducted the service from the quarterdeck of the Vanguard, which made a great impression on a group of captured French officers.[3]
After the battle the Vanguard headed for Palermo in Italy, where Nelson encountered Emma Hamilton and the crew languished there inactive for several months. On 5 June 1799, Nelson shifted his flag to HMS Foudroyant, with Captain Hardy and five lieutenants, and Comyn accompanied them until 1800. Comyn was on the captured Guillaume Tell until he transferred to HMS San Josef on 24 December 1800.
In Spring 1801 the British Fleet was in the Baltic for the attack on the Danes at Copenhagen where Comyn was chaplain on Nelson's ship, HMS St George. Nelson transferred to HMS Elephant for the battle, but it is not known if Comyn accompanied him.