In Jerusalem, Sharon Golban (Olivia Williams), an Israeli archaeologist, discovers an ancient skeleton in a rich man's tomb behind a hardware store run by Nasir Hamid (Makhram J. Khoury), a Palestinian. Father Lavelle (Derek Jacobi), a priest who is an expert on such matters, is brought in on the discovery. Meanwhile in Rome, Cardinal Pesci (John Wood) assigns Father Matt Gutierrez (Antonio Banderas), a Jesuit priest who once did espionage work as a freedom fighter in El Salvador, to stop the spread of information on the discovery lest it poison the faith of Christian believers.

The Body, written and directed by Jonas McCord based on a novel by Richard Ben Sapir, vividly conveys the explosive mix of faith, passion, and politics in Jerusalem, a city where Christians, Moslems, and Jews are often at each others' throats. When more signs point to the possibility that the skeleton may be that of Jesus of Nazareth (the coloration of the waist and leg bones indicate that the death was caused by crucifixion, and a gold coin found in the tomb is from the time of Pontius Pilate), Father Gutierrez finds himself pressured from all sides to act.

This challenge to the Christian belief in Jesus' resurrection causes Father Lavelle to have a breakdown. Meanwhile, other parties in the Holy City are ready to use the findings from the archaeological dig to advance their political purposes. These include Moshe Cohen (John Shrapnel), a Jewish bureaucrat from the Prime Minister's office, and Abu Yusef (Muhamad Bakri), a Palestinian leader.

The adversarial relationship between Sharon Golban, a scientist who believes in reason, and Father Gutierrez, who honors the inexplicable, is depicted with just the right amount of tension. The Body shows the difficulties that arise when political extremists try to use religious problems for their own benefit. It also celebrates Christian faith that endures doubt and withstands the manipulations of ecclesiastical power.