The allegory of the Martian
This novel is pretty obvious about its religious content—the reader is supposed to liken Mike's story to the story of Jesus Christ, because Mike is a religious martyr in the greater context of the plot. So when Mike comes to Earth from Mars, it is an allegorical allusion to Jesus's divine "incarnation" (because Christians believe Jesus "came from heaven" so to speak). There are lots of details to this allegorical comparison. Like Jesus, Mike's life is threatened by government interests. Like Jesus, Mike asks important religious questions from a young age. Like Jesus, Mike is open-minded and considered a heretic by conservative religious folks. Ultimately, the final comparison between Mike and Jesus is that Mike ends up being murdered for his open-minded religious beliefs, and he is raised to a position of power in heaven, literally. The comparison is sophisticated.
The symbolic meaning of Jubal
Jubal is Mike's foster parent who raises the boy in his giant mansion that he built by his excellence in various careers. Jubal is a successful doctor, lawyer, writer, and thinker, so Jubal represents something archetypal in Mike's story. Jubal represents that Mike will not be held back in any way by a lack of knowledge or leadership. Mike is able to reach his full potential because Jubal is an accomplished person and a natural teacher.
The royalty motif
When the astronauts bring back Michael from Mars, he is like a prince of the human race on that planet. He comes to the earth, and they acknowledge his official ownership of Mars. When they change their minds, it's purely to take the pressure off of Mike in the public sphere, as a service to Mike. When Mike starts a religion, he does it as if he is a king. His religious community is basically a harem of his closest friends and lovers, and he lives in absolute luxury. The point of this motif is that Mike understands something about his nature that most humans don't get to experience: true authority.
The allegory of the mystic heretic
So, the novel clearly shows that Mike is supposed to be modeled after the gospel, but within that Christian allegory, Mike fits a more specific allegory: The allegory of the religious heretic. Simply put, the allegory of the mystic or heretic is that some people accomplish a great deal of religious enlightenment and religious experience, and those people often clash with more conservative, dogmatic religious people. It's almost as if the mark of true enlightenment is to be martyred by the close-minded. This allegorical nuance gives the novel a gnostic feel.
The sci-fi motif
In this book, Mike dies and literally goes to heaven and is literally installed in the heavenly ranks as an archangel. That seems to show that this story is properly religious, but at the same time, it wears a lot of costume from the sci-fi genre. For instance, there is the idea of space travel, colonization of Mars, the discovery of a Martian race, the government conspiracy, and eventually, Mike's Martian magic—these are all instances of a science-fiction motif.
