Phocus The Roman Emperor Appointed The First Pope in 607 A.D.

In 607, the two Bishops ( Bishop of Alexandria and the Bishop of Rome) had a dispute over which Bishop would be superior.  The Roman Emperor Phocus declared that the Bishop of Rome, Gregory, would be the patriarch and superior which gave Gregory his title and authority from an earthly ruler, not by Heaven.  

Protestant Christian Understanding:  In 607, the two Bishops had a dispute over which Bishop would be superior.  The Roman Emperor Phocas declared that the Bishop of Rome, Gregory, would be the patriarch and superior which gave Gregory his title and authority from an earthly ruler, not by Heaven.  

Catholic Christian Understanding: An overwhelming majority of Protestant sects and historians agree that Phocas was not the power that gave Pope Gregory his position as the ultimate power as Pope, nor did Phocas ever declare he was responsible for making the first Pope.  During this time, the Bishop of Constantinople was declaring himself to be the head bishop of all the bishops in the East.  He was trying to proclaim he (The Bishop of Constantinople) was in charge of all the Greek speaking bishops and the Bishop of Rome was head of the all the Latin speaking bishops.  So it was the Patriarch of Constantinople, not Alexandria, that started to get "too big for his britches", as the saying goes, and was also the spark that started the schism where the Eastern churches split away all together.  

There was no dispute between the Bishop of Alexandria and the Bishop of Rome at all during this period, in fact, the Bishop of Alexandria was on the decline.  There were disputes between The Bishop of Rome and the Bishop of Constantinople and what Emperor Phocas actually did was confirm that the Bishop of Rome had already been declared by prior councils of having authority over all, including the bishops in the East. And again, I have to refer the reader back to the book "Documents Illustrating Papal Authority AD 96 - 454" by  the Protestant Edward Giles, who clearly demonstrates this in his unbiased and accurate research.  

All that Phocas did was say to the Patriarch of Constantinople that he was over stepping his bounds, his claim that he did not have to listen to the Bishop of Rome was wrong and that he being subordinate to the bishop of Rome had already been decided centuries earlier.  So Phocas did not hold any power to appoint anyone, nor did he claim he did. He was simply reminding the patriarch of Constantinople, who was the Bishop of his hometown, that he was under the Bishop of Rome's authority, and outside of that he was being disobedient.

In addition to this, there is clear and indisputable evidence that the Papacy existed.   Both the East and the West were recorded time and time again in the 300's, 400's, 500's, long before the 600's, that they all agreed the Bishop of Rome held authority over all.  The previous councils, which were all in the East and not in the West, all agreed that the Bishop of Rome presided over the council.  Pope Leo 1st sent his tome, or "to do list" of things to get done, to the council of Ephasis in 430 and Council of Chalsedon in 451, and Pope Leo the 1st decided and directed what issues needed to be addressed through his tome. When it was read out at the councils, all the Bishops stood up from both the East and the West and chanted, "Peter has spoken through Leo, this is the ancient beliefs of the Church, this is what we all believe, Amen, Alleluja!"  

More on proof the Pope lineage carried on after Peter can be found by the records of St. Augustine himself, a recognized Church founder by all:

(In his Easter letter of 367, Athanasius, Bishop of Alexandria, gave a list of exactly the same books as what would become the New Testament canon,[ and he used the word "canonized" (kanonizomena) in regards to them.  The first council that accepted the present Catholic canon (the Canon of Trent) may have been the Synod of Hippo Regius in North Africa (AD 393); the acts of this council, however, are lost. A brief summary of the acts was read at and accepted by the Councils of Carthage in 397 and 419. These councils were under the authority of St. Augustine, who regarded the canon as already closed. Pope Damasus I's Council of Rome in 382, if the Decretum Gelasianum is correctly associated with it, issued a biblical canon identical to that mentioned above, or if not the list is at least a sixth century compilation. Likewise, Damasus's commissioning of the Latin Vulgate edition of the Bible, circa 383, was instrumental in the fixation of the canon in the West. In 405, Pope Innocent I sent a list of the sacred books to a Gallic bishop, Exsuperius of Toulouse. When these bishops and councils spoke on the matter, however, they were not defining something new, but instead "were ratifying what had already become the mind of the church."

2nd Century Church Father, Irenaeus Bishop of Lyons wrote a book in 175 AD called "Against the Heresies".  He explains tradition and scripture which shows the papacy line from Peter all the way to the Pope then.  Both Protestants and Catholics agree he was one of the crucial founding Fathers of the Church.  The list of Popes can be found anywhere today by a simple Google or in any Church history documents.  Many Protestant denominations do not deny this.  Irenaeus Bishop of Lyons details the list of all the Popes since Peter and did this in 175 AD for public record for all to see.  He also instructed that all churches must agree with the Roman Catholic Church since it holds the preeminence. 

I would also like to recommend a book used in my study which is a Protestant book that explains the lineage of the Papacy all the way back from Christ, the book is called The Oxford Dictionary of the Popes by J.N.D. Kelley, who is another Protestant historian that is very credible and widely accepted.  In his work, he gives articles on all the popes in chronological order Since Peter.  As a Protestant scholar, he does not accept or recognize the power of the papacy but does completely acknowledge the legitimacy of the Papacy line starting with Peter and his successors all the way to his time.  The historical data and facts  on the Papacy lineage is undeniable in many Church documents, just as Kelley shows in his work.