I am afraid that I am less and less certain how I ought to pray in the midst of the crisis in the Church. Fortunately, this is a situation anticipated by St. Paul: nam quid oremus, sicut oportet, nescimus: sed ipse Spiritus postulat pro nobis gemitibus inenarrabilibus. In any case whatever we think or say, we have to pray: fiat voluntas tua. Most of the time I pray for the unity of the Church, the very thing that attracted many of us to the Church, the very thing I prayed for before I entered the Church.  But it cannot just be a partisan exercise, nor a naive demand for Reunion All Around. Speaking of which, Fr. Ronald Knox is helpful, preaching at the end of the war in Europe:

“Again and again you will find the language of the sacred liturgy dominated by this idea of oneness in Christ; a supernatural oneness which triumphs over every disparity, every separation. That is, I think, the idea which underlies one of the most beautiful, and at the same time one of the most obscure, petitions which we make during Lent; when we ask almighty God ut congregata restaures, et restaurata conserves, "that thou wouldst bring together and mend, mend and forever preserve, what now lies broken".

Congregata restaures, et restaurata conserves; the Church, knowing well what we are, members of a fallen race, does not simply ask God to keep us in our present position, and leave it at that. She knows that that will not do, we are scattered all over the place, like broken pieces of china, and we have got to be put together again before we can be worth preserving. No, we must not be so miserably small-minded in our prayers as to tell God that we want him to keep the world just as it is, a mass of quarrels and seething discontents, if only we can have five or ten years of peace before hostilities start again. We must ask him to gather up the broken pieces of our world and cement them together again in some kind of world order, based on real justice. . .  But there is more behind it. If we will be honest with ourselves, we shall admit that the war has brought disharmony into your life and mine; we are not at peace in ourselves.