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.
The transepts of Thomas's church appear to have been without aisles. The remains in the crypt show that there were two eastern apses to these transepts close to the central tower, and Professor Willis deduces from the position of these apses that they left no room for eastern aisles. There is no instance in existence of a transept having western without eastern aisles. One may therefore conclude that aisles were entirely wanting. Professor Willis thinks it possible that an additional pair of apses may have existed on the east side of these transepts, to the north and south respectively of these already discovered. This was certainly the case in St. Mary's Abbey.
As has been mentioned, considerable doubts still exist as to the size and character of the choir of Thomas's church.
On the one hand we have positive testimony that Thomas rebuilt the whole church; on the other, the walls of the crypt, as they existed up to the time of Roger's choir, are a part of the Saxon church. Their masonry is Saxon, and they mark the lines of a chancel far too narrow to have been that of Thomas, even if we suppose that his choir was necessarily small, from the want of funds at his command, and the wasted condition of the diocese.
This would seem to support the theory that Thomas left the Saxon choir as it was, and contented himself with rebuilding the ruined nave and transepts. In that case, of course, the Saxon choir remained until the time of Roger.
The alternate theory is that Thomas rebuilt an enlarged, but still a small, choir, leaving the Saxon crypt as it remains to this day; and that even this choir proved too small for the magnificent ideas of Roger, who utterly demolished it to make room for his own great building, leaving no trace of it above ground. This is the more probable supposition, and it is supported by the fact that the inner wall of the crypt is composed of fragments of masonry, buildings, etc., of early Norman date, which might well be parts of Thomas's choir, if it was destroyed, as we suppose. Some of the stones are covered with white plaster, showing they are parts of the interior of a building, and they are of the same red sandstone as the remains of the transept apse, which was undoubtedly built by Thomas.
As has been said, the choir of the minster remained unusually small for so important a church. The eleventh and twelfth centuries were periods of great activity in church building, and many of the Norman architects planned their works on a vast scale. With the examples of Durham, Winchester, and St. Albans before them, it was natural that the archbishops of the Metropolitan Church of York should be dissatisfied with the size of their own choir. It fell to the lot of Roger, the rival of Thomas à Becket, to rebuild it. The date of his nave is approximately 1154-1181. The remains of his work in the crypt show that it was in the latest style of Norman architecture and considerably influenced by Flambard's work at Durham, with channeled and fluted pillars. The detail appears to have been richer and later in character even than Flambard's. The outer wall of the crypt shows the dimensions of this choir. It was square at the end, and had flanking towers—two bays from the east—which served as transepts inside. The eastern transepts of the present choir still keep the position and tradition of these towers. The aisle probably ran round the east end as at Romsey and Byland. The two bays east of the tower were wider than the others. Roger, it should be said, had been Archdeacon of Canterbury, and he was therefore well acquainted with the "glorious Choir of Conrad" built by Anselm. There is much in the planning of his work to show that he was influenced by the example of Conrad's choir.