Life in Australia is described at length in the novel, telling little vignettes about people trying to get along in a colony of convicts and criminals, but the story is focused on Farquhar and Baker, two Australian Brits who are struggling to figure out what life will be like in this strange, exotic place. Out of these two characters, Farquhar is the more important, since the title of the book refers to him. By comparing their points of view, the reader sees that the basic dilemma of human life has not changed; even in Australia, there are right decisions and wrong decisions.
For Baker, the line between right and wrong becomes blurred very quickly. First of all, he's so far away from his wife that there is absolutely no chance of him being caught, so he thinks about cheating on her a lot. He is firmly committed to resist that obvious temptation, but when he meets Mary, he can't help himself. His opinion becomes compromised, and he allows himself to have both women. Then, he shows the audience the truth of his corrupt character at the end when he leaves his new wife to fend for herself with their child in her womb. In other words, he is as corrupt and evil as the rest, but he was making excuses for himself along the way.
Farquhar is less swayed by circumstance, so his opinions are more foundational. He criticizes not the penal colony itself, but rather, he criticizes the legal and justice systems of Britain for such an invasion of free will. He wonders about the legitimacy of British colonies abroad, and he starts figuring out that there are specific people making lots of money while other people are left to struggle and die on new continents.