The state of Code 46 is, to a large extent, a totalitarian one. It maintains strict control over both the travel and reproduction of its citizens. It is not however, the wholly nefarious entity so typical of science fiction dystopias. It is not controlling its citizen's lives in order to fulfill its own selfish desires for capital or power. Neither is it unsympathetic towards its citizens: while it may act contrary to their desires it does so in order to protect what it considers to be their best interests - travel restrictions for example serve the function of protecting public health. For Robbin's character it fulfills the functions traditionally given to the wife in infidelity dramas. It is the loving, nurturing, familiar embrace of a life partner: an embrace that can also begin to feel stifling.
However it's not simply designed to serve a dramatic function: it's also intended as a comment on the nature of state power and that long-running debate as to just how large government should be and how much control it should have over our lives. In Code 46 the conflict between the state and the individual is expressed in individuals who desire something dangerous or forbidden, who know and acknowledge the potential consequences and yet are determined to fulfill their desire anyway - having reasoned that the benefits outweigh the potential consequences. In doing so they are set against a state which believes the risks to the individual, and potentially the broader society, are too great to risk.
Unusually for a western dystopia the film does not come down firmly on the liberal side of the argument. On the one hand Damian's caving expedition does offer him a sense of joy and fulfillment that his ordinary life does not. However in a stark warning to our newly corrupt protagonist his medical condition does rear its head in a brutal fashion and he dies in agony on a hotel room floor: his bats unseen, his desire unfulfilled. It's difficult to argue that the state's judgement was wrong - although whether keeping such a tight leash on the population as a whole is worth avoiding occasional accidental deaths is something that liberal viewers could be expected to question.
And it's something that the second rebellion does question more starkly. Despite the fact that their incestuous love is breaking every taboo in the book one can't help but wonder just how convincing the argument against it is in this future society. The presence of large numbers of clones suggests that reproduction is no longer solely and perhaps is rarely the result of intercourse, contraception is highly effective and there's no suggestion that abortions have any sort of stigma attached to them. Furthermore the unsettling emotional territory of the boundaries of family relationships being crossed is nearly entirely removed. Does the state forbid such contact to maintain social cohesion?
In any case the film makers do attempt to make the viewers sympathize with the lover's plight - something of a Herculean task given that, in opposition to standard dystopian tropes, their relationship (adulterous, incestuous) is something that even a modern viewer in a liberal nation would struggle to cope with and which is outlawed in most (all?) nations in which they live. The question it raises is that, even if the government is right, does it have the right to extend its control into such personal areas in such an all encompassing and unsettling manner?
(The way the state is portrayed as diffuse and yet is humanised and the way its control manifests itself are subjects for part 3)