After the Saxon invasion had concluded and Saxon kingdoms had been established the Celtic Church began to re-establish itself in Celtic lands that were now inhabited by Saxons. As they began evangelizing to the Saxons they discovered they had competition from the Roman Church. Between 595 and 600 A.D. the church in Rome sent missionaries to establish a church in England. Those missionaries were welcomed at St. Martin’s Celtic Church in Canterbury. It wouldn’t be long before the two churches would become competitors in converting the pagan Saxons. As the pagan Saxons were converted to Christianity they were forced to choose between the Celtic Rite and Rome. The Celtic Church and Roman Church were very different, not only in the way they worshipped, but in the way they were structured as well as other important matters, such as when the church celebrated Easter. The Saxons were confused and asked if Christians had the same God, one God, then why were there such dramatic differences. This resulted in a series of councils between the two churches to try and work out their differences.

In 603 a council was convened at Augustine Oaks on the Severn River to work out the differences between the two churches. The Roman Church demanded obedience to the Bishop of Rome. Rome’s representative, Augustine was plainly told that “the Celtic church would acknowledge no man as supreme in the Lord's vineyard”. Christ was the head of the church, not the pope. Two subsequent councils were held without resolving the differences. But, the councils did agree on one thing, that Celtic Christianity came from Jerusalem and not from Rome.

In AD 657, Abbess Hilda had founded a double monastery of both monks and nuns at Whitby (Streoneshall) in the Saxon province of Northumbria. Hilda was a patroness of the arts and a notable teacher, whose advice was sought by Kings and Abbots alike and her monastery became known as a center of learning. In AD 664, she played hostess to the famous Synod of Whitby in which the path of the Northumbrian Saxon Church was debated. The Roman Church likes to cite the Synod of Whitby as the council where representatives from Rome and the Celtic church met to decide the fate of the Celtic Church. In reality it had nothing to do with any country (here Britain) choosing Rome's version of Christianity over the Celtic Church. The Celtic Church was made up of many autonomous churches and monasteries and it was not possible for any representative to sit down at a council and bind the whole church. What the council was called for was to settle the debate over differences between the two churches such as when to celebrate Easter and other minor practices within the Saxon Church of the region of Northumbria. The effect of the decision was limited only to the church in the Saxon province of Northumbria as other Saxon provinces were under the rule of other kings. Both the Celtic Church and Rome had missions in Northumbria. The Northumbrian church chose the Roman calculation for Easter, because that was the method endorsed at the Council of Nicea although the Celtic and Mesopotamian Churches rejected this calculation (Eusebius, Ecclesiastical History). However, something the Roman historians often neglect to mention is that the Northumbrian Church adopted the Celtic Rite for their services.

There are two interesting historical accounts, one from Eddius Steppanus's Life of Wilfrid and Bede's Ecclesistical History, that report of a terrible plague that began in the south and swept up through Northumbria killing many Roman priests and bishops, including the newly installed Roman bishop of Northumbria shortly after the conclusion of the Synod of Whitby.

The Roman Church likes to point to the synod as a pivotal point in Celtic Church history and say the church simply dissolved after the council. Bede may be responsible for spreading this misconception. He writes of St. Colman throwing his hands up in despair after the council, resigning his see at Lindisfarne and returning to Scotland. he did not want to celebrate what he considered to be a pagan calculation of Easter. St. Colman didn’t want to be a part of celebrating Easter based on a mathematical calculation of moon cycles that was tied to the Saxon pagan fertility goddess, Oestre.

The Church of England in recent years has put yet another spin on the synod (from their webpage). They report the synod as a cordial meeting of the two churches and the Saxons whereby they mutually agreed to all merge into one church, which was the Church of England. According to them, the Church of England did not begin with Henry VIII, but through the accord which came out of the Synod of Whitby, in which the three streams of Christianity were merged to form their church. The fact is the Synod of Whitby had no effect on the existence of the Celtic Church, which continued past 664, the date of the council. The Church did not merge with the Roman and Saxon church to form the Church of England, nor did it simply dissolve. It continued strongly in Scotland, Ireland, Brittan, Wales and the Outer Hebride Islands and maintained a presence in Saxon England, albeit a much weaker one due to the Saxon’s pushing the Celts outward. There are many Celtic missals (liturgy books) on display at university museums in Scotland and Ireland which attest to the continuation of the Celtic Church beyond 664, including the Book of Kells from the 8th century, the Book of Deer and St. John Mulling from the 10th century. All of them are later than the date of the council proving the Celtic Church did not disappear as Rome maintains.