On the whole, therefore, it is perhaps most probable that the church referred to by Flaccus Albinus was the minster. If that is so, this church remained until it was ruined by the Danes in 1069. Then it was certainly either wholly or partially burnt down. Thomas, the first Norman archbishop, appointed in 1070, found the minster, the city, and the diocese, all waste and desolate. At first he was satisfied with roofing in what remained of the cathedral and otherwise restoring it as best he could. Afterwards, before 1080, he began to rebuild it. It is uncertain whether he rebuilt the whole church, or merely the nave and transepts.
Stubbs on this point seems to give two different accounts.
"Thomas," he states, "restored the canons of the church after he had rebuilt it as well as he could." Afterwards he says, "He built the church as it now is from its foundations."
Probably, this first passage refers to the immediate repairs which Thomas found necessary in 1070, and the second to his ultimate rebuilding of the church.
William of Malmesbury says that he began the church from its foundations and finished it. In the face of this positive testimony it is probable that Thomas built not only the nave but the choir. That he did so has been doubted, because the choir of his day was undoubtedly a very small one, and was afterwards demolished by Roger. It must, however, be remembered that Lanfranc rebuilt Anselm's Norman choir at Canterbury in the same way. It is very likely that Thomas was forced by necessity to plan his work on as modest a scale as possible, and that the pride of Roger would not allow the choir of his minster to remain one of the smallest in the cathedrals of England.
The minster, as Thomas left it, was utterly unlike the present church. The nave was probably shorter than the present one, and was certainly twenty feet narrower. This was discovered after the fire of 1840, when remains of the side aisle walls of Thomas's nave were discovered. There are no data for the number of piers in this nave or for the position of the west front.
The tower certainly stood on the site of the present tower, as Roman ashlaring has been discovered on the north-west side of the north-west tower pier, above the vault of the side aisle, and also portions of a shaft with a base, which probably belonged to the Norman clerestory. It will be seen that the present piers supporting the central tower contain cores of Norman work recased in Perpendicular times.