Holy Trinity is the story of two priests, FATHER HARLEY JACKSON and FATHER WETHERBY-SMYTHE. Both the priests are unconventional, Harley Jackson being a former Hells Angel and Sebastian Wetherby-Smythe a self-professed Gay. Their church has almost no congregation, except for a dreadful organist and an elderly lady who is a compulsive confessor. Knowing that their church may be closed down, the two priests decide to rent it out to raise some extra cash.
Bishop O'Toole hates the two priests, and is obsessed with the idea that the Holy Grail is hidden somewhere inside St Xavier's. He is desperate to have the church closed down and is in collusion with the corrupt Town Mayor, JASPER HARPER. Jasper Harper owns land behind St Xavier's, and wants the church demolished so that he can build a golf course.
Swami Gupta Raj is a Hindu, and he uses the spare bedroom in his house as a Hindu Temple. His dominating wife wants the room back to use as a spare bedroom for a visiting guest from India. She has an idea that the guest, RAVI, will be a suitable husband for her daughter JAMILLA RAJ.
Rabbi MANNI MANNHEIM sees his synagogue bulldozed to the ground. Jasper Harper has used his power as Mayor to have the building condemned, and wants the land to build a golf shop for his new golf course.
JOSHUA MANNHEIM is the Rabbi's son. He is a photographic journalist and works with Jamilla Raj, who is also a journalist with the local newspaper, the Herald. Between them, they uncover the real reason behind Jasper Harper's plan to build a golf course. They discover that he already owns a golf course, and he has dumped toxic waste into the landfill as it was being built. With the help of BONES, one of Harley Jackson's old biker friends, who is also a computer-hacking expert, they find that the Bishop has taken a bribe from Jasper Harper to ensure that the church is closed down.
The Swami and the Rabbi rent out the church for their respective places of worship. The two priests have to then juggle the situation between the Rabbi and Swami, as well as their own Catholic services. In an attempt to swell the congregation, they call upon their friends. Sebastian Wetherby-Smythe asks his gay community to come to church, and Harley Jackson asks his brother THOR, who is still running a Hells Angels club, to get his friends to fill the church. Chaos ensues as they try to deceive the Bishop.
Harley formulates a plan to expose the Bishop's true reasons for wanting the church closed. He plants a fake Holy Grail inside St Xavier's, and the Bishop takes the bait with disastrous consequences.
Eventually, both the Bishop and the Mayor are exposed. St Xavier's is saved. The church is renovated, and additional wings are built to accommodate a Hindu Temple and a Synagogue.
Jamilla and Joshua, who by now have fallen in love, get married. They hold marriage ceremonies in all three places of worship – the synagogue, the Hindu temple and the Catholic church. All ends happily.
