Thy Will Be Done is the story of Pius (Ramsey Nouah), a happily married pastor in charge of a large church in Lagos, Nigeria. But when his first wife (Mary Njoku) that he buried 7 years ago suddenly shows up, his world is thrown into turmoil. His present wife (Mercy Johnson) tries to fight her corner but Pius has a choice to make…between his calling and his wives; between old sins and new loyalties; between taking firm action and surrendering to God’s will. Weakened by guilt and overwhelmed by sensational revelations, nothing would have prepared Pius for how rapidly things would descend into violent chaos…for hell hath no fury like a woman scorned.
The film opens with a scene of a happy and successful community as they share their lot with one another, but there is a sudden turn of event as three strange beings invade the kingdom in search of an antique; which has the power to protect its people and sustain its royalty. The kingdom’s warriors are overpowered and the invaders take away the sacred emblem, thereby bringing a curse on the land.
A young man, Kunle (Saheed Balogun) commits a grievous act that leaves his family members in anguish. In Lagos, Kunle hides cocaine in his mother's (Lanre Hassan) baggage before she pays a visit to his siblings, including the eldest brother Femi (Sola Fosudo) in London. His mother narrowly escapes from the British immigration officers.
The film narrates the story of identical twins, Taiye and Kenny (Ramsey Nouah). Taiye is based in Lagos with his wife, (Stella Damasus) and his three children while Kenny is based in London. The agony of a marriage without children, after several years frustrates Kenny to convince Taiye to come to London in other to impregnate his wife due to his (Kenny) low sperm-count. However, more problems result.