In a section called “objections to prayer” (2727) the Catechism remarks:
[S]ome would have it that only that is true which can be verified by reason and science; yet prayer is a mystery that overflows both our conscious and unconscious mind.
oratio mysterium est quod nostram conscientiam nostrumque inconscium superat animum
“Mystery” in the Scriptural sense is not a baffling or unintelligible object or proposition but an ongoing and therefore incomplete revelation. This ongoing revelation will always have something unintelligible and baffling about it, but this is not because God had any interest in being baffling or unknown (since revealing yourself and your plan for the universe is a pretty stupid way of going about this) but rather because he respects the developmental and historical nature of creation. Like everything else in time, revelations in time evolve, grow, mature, and develop. Mystery is therefore the opposite of obscurity – it is a sort of education.
In one very important sense mystery has ceased with the Incarnation, since there is a definitive sense in which revelation cannot develop beyond this. Mystery only exists now so far as we see the Incarnation in relation to its eschatological revelation of judgment, in its sacramental or Scriptural hiddenness, or in its relation to the progressive dispelling of obscurity from the minds of the members of the Church. The mystery of prayer seems to map best over this last sense of mystery.
But why speak of prayer as a mystery that overflows (an exactly right translation of superare in this context) the conscious and unconscious mind?
The unconscious mind is the confederacy of unknowable but properly human conditions placed on human thought. These conditions are either natural or (in some way or another) constructed. We cannot cannot help thinking of things as finite, temporal, spacial, numerable, repeatable, etc, and this natural habit habit remains even in thinking of individuals, forms, souls, human persons, angels, and the Trinity. This is why we don’t know metaphysical things by abstraction but only by a judgment that negates an unconscious condition put on the objects we know. Less universally, the unconscious involved the conditions of what Wittgenstein called the background understanding. I can’t help thinking that when I look around I’m seeing the natural world, and that the supernatural must somehow intrude into this. I know this is a particular, contingent and historically variable background understanding, and I can even experience it as inadequate (the experience of mass, or the Muslim call to prayer don’t make much sense on this bifurcation) but I still can’t help working within this background in my own life.
The Cathechism speaks of prayer, in opposition to reason and science, as overflowing these human conditions placed on human thought. It can fill up a philosophy or discourse on nature but never be captured by them. The reason for this is given earlier in an account of contemplative prayer, which describes it not the attaining of an abstracted or separated object or the penetration into it, but as
“[N]othing else than a close sharing between friends; it means taking time frequently to be alone with him who we know loves us.” Contemplative prayer seeks him “whom my soul loves.” (2709)
Among human friends, there is always the equality of nature, which requires that their interior life be articulated and shared only by way of signs for abstractions and separations. The friendship of prayer is not like this, and so is an education overflowing the conscious and unconscious mind.