The second season carries on with the error prone lives of three priests living with their housekeeper in Ireland on the bizarre Craggy Island. The three Fathers disastrously attempt to rig a raffle, make efforts to give-up their vices for Lent , adopt a pet rabbit, and occasionally tend to matters of the soul.
Ted, Dougal and Jack go on an all-expenses-spared holiday to Kilkelly Caravan Park. They meet a young couple, and are soon in trouble with the police. Entertainment comes in the shape of St Kevin's Stump and the Magic Road. Father Jack goes missing; Father Noel Furlong and his youth group turn up to put the final nail in the coffin of the holiday.
The roof of the Parochial House is leaking, and Ted decides on a raffle to raise the funds, with a car as the prize. Unfortunately, an accident with a cyclist puts something of a dent in the vehicle. A similar car is borrowed from the Dancing Priest in order to save the raffle; however, the priests must then win in order to return the car. Despite this intrigue, the roof does not get repaired.
The Holy Stone of Clonrichert is to be upgraded to a class 2 relic, and unfortunately this entails three Bishops visiting the island - Father Jack must be housetrained quickly. Only one of the bishops dies - Ted therefore considers this to have been a relatively successful visit.
Ted goes on a picnic, Mr Benson's whistle is stolen and Dougal learns an important lesson about true friendship. Ted narrowly avoids incriminating himself to save Dougal's worthless hide
Fathers Ted and Dougal enter A Song For Europe with My Lovely Horse. The tune is stolen from the b-side of a Norwegian song that didn't even win A Song For Norway but the lyrics are all their own work. Somehow they get through to Eurovision and score.... nil points.
Rabbit-phobic Bishop Brennan pays a visit to investigate reports of Father Jack sleepwalking naked. Unfortunately Dougal has overrun the house with rabbits, and a Terry & June-style farce ensues as Ted and Dougal attempt to keep Father Jack in bed, and the ever-multiplying rabbits away from the bishop.
Ted is asked to compere the 'Lovely Girls' competition while Dougal is left in charge of the house. Father Jack is mistaken for Bob Geldof and Dougal manages to give the house away to a feminist rock star called Niamh Connolly. Ted has to get the house back, but how will this affect his dinner plans with the winner of the 'Lovely Girls' competition?
Ted and co. enter a giving-things-up-for-Lent contest and soon discover that abstinence is easier preached than done. Father Jack sobers up for the first time in years, but Dougal and Ted find their resolve wavering. To strengthen their vows Ted calls in a nun to supervise them. She turns out to be a sadist of the first water, and the results are inevitable.
After discovering Father Jack is suffering yet again(!) from "hairy hand syndrome," Ted is delighted to send Jack, by "doctor's orders," to St. Clabberts Old Folks Home (otherwise known as 'Jurassic Park'). Unfortunately, Jack's replacement happens to be one of the nastiest priests ever - Father Fintan Stack. Along with his disregard for the church, Stack has a rather irritating habit of playing jungle music loudly at 3 o'clock in the morning, and a plan is hatched to get Jack back to sort out Stack.
Ted and co. end up being crammed in a plane along with every other priest who has appeared in their lives after a visit to the Shrine of Kinlettle. In a fit of the usual stupidity, Dougal manages to empty the fuel tanks on the plane. To make matters worse, there are only two parachutes to go around many more priests, so Ted devises a way for the priests to compete for the parachutes. Unfortunately, Jack has other plans for the parachutes.