Moreover, flooded with a new spirit, Francis frequently entered a certain cave, while his companion entered outside, completely ignorant of what Francis was doing inside. There, in secret, Francis prayed with tears to his heavenly Father that, as his guide on his way, he might show him his will more clearly. Thus praying at great length, he harshly afflicted himself, and until he knew by divine inspiration how he should begin, the distraction of his changing feelings would allow him no rest. There alternated within him happiness for the sweet taste of the spirit, the gravest sorrow for sins of the past, not a little fear of the future, and a fervent desire for what he had begun. (The Life of St. Francis by Julian of Speyer, chapter I)
But the caves into which we go to allow ourselves to be found by God are also the empty darknesses of ourselves. By reducing our attachments to created things and our appetites for them, we begin to empty ourselves that we might be filled anew by God. This is what John of the Cross calls the active Night of Sense.
As Edith Stein points out, following John, this makes caves out of our interior faculties:
The first cave is the intellect, its emptiness is a thirst for God and it longs for divine wisdom. The second cave is the will, which hungers for God and clamors for the perfection of love. The third cave is the memory. It is consumed with the desire for the possession of God. (The Science of the Cross, 207)
The incarnation has made the human person the locus of saving sacrifice. The humanity of Christ is the New Temple. As members of his body by our baptism into his death and resurrection and our communion with him in the Eucharist, our individual personhoods also become that Temple. But we must also remember that when the Temple was rebuilt after the Captivity the Holy of Holies remained empty. The Ark of the Covenant was gone. The space was filled only with God's own silent and invisible Presence.
If we are to be Temple wherein the Presence of God abides and perfect Sacrifice finds a home, we too must empty ourselves and then enter into the emptiness in prayer. It is there that we will find the sweetness of the Spirit and the burning desire for our vocation.