The Ball and the Cross starts with a prologue in a flying ship made by a Professor called Lucifer. He is discussing the real truth with a man of religion a pastor called Father Michael. Father Michael believes in religion while the Professor believes in science. The ship runs into a ball and a cross over a Cathedral, where Lucifer pushes Father Michael out on a rooftop in anger caused by their argument. He is then escorted to an asylum, as the people he meets are sure he is crazy.
We are then sent to the life of Evan McIan, another strong believer. When he is walking around the streets and sees a shop with posters that go against his beliefs, which is why he shatters a window. He is caught and brought to court against the owner of the shop. They are both set free, as the owner says he would never duel a religious man such as Evan; he would rather be deemed a coward.
As both the men are released, the shop owner says he would accept the duel after all. They go to a shop to buy equipment, and law enforcement are once again after them, as the shop owner realizes what they were going to do. They then begin running away from them together, and they stop disliking each other as much as they did before.
They are suddenly taken into an asylum that puts them in a cell. They manage to escape from their cells, and as they head out see that many of the people they met on their way to the asylum are there as well. The leader of the asylum wants them to forget that they ever met Evan and the shop owner. The asylum begins burning, and the last scene is of a flying ship that lowers, dropping two doctors before flying away.
