At this time of change for the Roman part of the Catholic Church, it seems appropriate to pray for the whole church on earth: the "church militant" (as opposed to the "church triumphant" consisting of those who have died and are awaiting the resurrection of their bodies at the return of Christ to the earth).
So, in powerful (if somewhat archaic) words from the Book of Common Prayer (1662)...
Let us pray for the whole state of Christ's Church militant here in earth.
Almighty and everliving God, who by thy holy Apostle hast taught us to make prayers and supplications, and to give thanks, for all men: We humbly beseech thee most mercifully to receive these our prayers, which we offer unto thy Divine Majesty; beseeching thee to inspire continually the universal Church with the spirit of truth, unity, and concord: And grant, that all they that do confess thy holy Name may agree in the truth of thy holy Word, and live in unity, and godly love.
We beseech thee also to save and defend all Christian Kings, Princes, and Governors; and specially thy servant ELIZABETH our Queen; that under her we may be godly and quietly governed: And grant unto her whole Council, and to all that are put in authority under her, that they may truly and indifferently minister justice, to the punishment of wickedness and vice, and to the maintenance of thy true religion, and virtue.
Give grace, O heavenly Father, to all Bishops and Curates, that they may both by their life and doctrine set forth thy true and lively Word, and rightly and duly administer thy holy Sacraments: And to all thy people give thy heavenly grace; and specially to this congregation here present; that, with meek heart and due reverence, they may hear, and receive thy holy Word; truly serving thee in holiness and righteousness all the days of their life.
And we most humbly beseech thee of thy goodness, O Lord, to comfort and succour all them, who in this transitory life are in trouble, sorrow, need, sickness, or any other adversity.
And we also bless thy holy Name for all thy servants departed this life in thy faith and fear; beseeching thee to give us grace so to follow their good examples, that with them we may be partakers of thy heavenly kingdom:
Grant this, O Father, for Jesus Christ's sake, our only Mediator and Advocate.