That which is born alive was, by the law of the Church and the law of Nature, suffered to live, and helped to maturity if possible, by those who had begotten it. (1.3)
The Church commands its version of morality be observed in the case of mutant births. This is a small point early in the novel, but it grows to become a source of much contention between Church, state, and individual later on. Keep it in mind, Shmoopers.
There was nothing to do but obey the command to return.
Francis's will has been completely consumed by the Church and its commands. To question his superiors is to question the Church—something he cannot do.
Father Cheroki, who came of baronial stock from Denver, tended to react formally to men's official capacities, tended to speak courteously to the badge of office while not allowing himself to see the man who wore it, in this respect following the Court customs of many ages. (4.2)
The Church claims the moral high ground of God. And whether or not it owns that moral high ground, it's still an organization made up of mortal men on Earth. Father Cheroki's inability to see this fact grants the reader the ability to do just that. That's dramatic irony for you, and it's awesome.
But I, too, am a member of a oneness, thought Dom Paulo, a part of a congregation and a continuity. Mine, too, have been despised by the world. Yet for me the distinction between self and nation is clear. (16.92)
Like Francis before him, Dom Paulo has become part of a whole. He lets that "oneness" have power over him. But unlike Francis, Dom Paulo understands how institutions can take over your own interests, and willfully chooses the Church over the government.
"To serve God first, or to serve Hannegan first—that's your choice."
"I have little choice, then," answered the thon. "Would you have me work for the Church?" The scorn in his voice was unmistakable. (21.73-74)
Taddeo is Dom Paulo's foil for many reasons. This is one. Like Dom Paulo, Taddeo made a choice to let an organization have power over him, and he made that choice willfully. He simply chose differently than Dom Paulo; he chose the state.
"Let's be frank with each other, Father. I can't fight the prince who makes my work possible—no matter what I think of his policies or his politics. I appear to support him, superficially, or at least to overlook him—for the sake of the collegium." (21.59)
The state is gaining power, and that puts it in direct competition with the Church. It's like one is Batman, the other is the Joker, and we're all stuck in the middle.
"They can know it by the children they beget and send to asylums for the deformed. They know it, and they've kept the peace. Not Christ's peace, certainly, but peace, until lately—with only two warlike incidents in as many centuries. Now they have the bitter certainty. My sons, they cannot do it again. Only a race of madmen could do it again—" (25.154)
Note the passage of "not Christ's peace." It's a small hint of how far Church and state have separated since the beginning of the novel. Now, they can't even agree on how to go about being peaceful.
"'The provisions of Public Law 10-WR-3E in no way empower[s] private citizens to administer euthanasia to victims of radiation poisoning. Victims who have been exposed, or who think they have been exposed, to radiation far in excess of the critical dosage must report to the nearest Green Star Relief Station.'" (27.5)
The state gets in on the church's game. Just like in our first quote—the one we told you to keep in mind—the state begins administrating rules for who should be allowed to die, how they should be allowed to do it, and even where they can do it.
But one of the officers snapped out into the slow lane just ahead of them and pointed his traffic baton at the vehicle's obstruction detection; the autopilot reached automatically and brought the car to a stop. (28.128)
In Francis's day, the Church had all the power; they had the Memorabilia and a vice grip on education. Now, the tables have turned. Thanks to technology, the state can quite literally control the destiny of others.
"Get back in the car," Dom Zerchi told her. "You cut that tone of voice, mister!" the officer barked. "Lady, what about the kid?" "We're both getting out here," she said. (28.147-149)
The Church, state, and individual are all represented in this final fight to determine the fate of a mother and her child. Although the state wins this round, the novel doesn't seem to suggest either Church or state was right. It leaves that question open for you to ponder. Yay, pondering.