Probably from about 1190, Gilbert de Glanville (bishop 1185–1214) commenced the rebuilding of the east end and the replacement on the monastic buildings.
The north quire transept may have been sufficiently advanced to allow the burial of St William of Perth in 1201, alternatively the coffin may have lain in the north quire aisle until the transept was ready.
It was then looted in 1215 by the forces of King John during siege of Rochester Castle.
Edmund de Hadenham recounts that there was not a pyx left "in which the body of the Lord might rest upon the altar".
However, by 1227, the quire was again in use when the monks made their solemn entry into it.
The cathedral was rededicated in 1240 by Richard Wendene (also known as Richard de Wendover) who had been translated from Bangor.

The shrines of Ss Paulinus and William of Perth, along with the relics of St Ithamar, drew pilgrims to the cathedral.
Their offerings were so great that both the work mentioned above and the ensuing work could be funded.

Unlike the abbeys of the period (which were led by an abbot) the monastic cathedrals were priories ruled over by a prior with further support from the bishop.
Rochester and Carlisle (the other impoverished see) were unusual in securing the promotion of a number of monks to be bishop.
Seven bishops of Rochester were originally regular monks between 1215 and the Dissolution.
A consequence of the monastic attachment was a lack of patronage at the bishop's disposal.
By the early 16th century only 4% of the bishop's patronage came from non-parochial sources.
The bishop was therefore chronically limited in funds to spend on the non-monastic part of the cathedral.

The next phase of the development was begun by Richard de Eastgate, the sacrist.
The two eastern bays of the nave were cleared and the four large piers to support the tower were built.
The north nave transept was then constructed.
The work was nearly completed by Thomas de Mepeham who became sacrist in 1255.
Not long after the south transept was completed and the two bays of the nave nearest the crossing rebuilt to their current form.
The intention seems to have been to rebuild the whole nave, but probably lack of funds saved the late Norman work.

The cathedral was desecrated in 1264 by the troops of Simon de Montfort, during sieges of the city and castle.
It is recorded that armed knights rode into the church and dragged away some refugees.
Gold and silver were stolen and documents destroyed.
Some of the monastic buildings were turned into stables.
Just over a year later De Montfort fell at the Battle of Evesham to the forces of Edward I. Later, in 1300, Edward passed through Rochester on his way to Canterbury and is recorded as having given seven shillings (35p) at the shrine of St William, and the same again the following day.
During his return he again visited the cathedral and gave a further seven shillings at each of the shrines of Ss Paulinus and Ithamar.

The new century saw the completion of the new Decorated work with the original Norman architecture.
The rebuilding of the nave being finally abandoned.
Around 1320 the south transept was altered to accommodate the altar of the Virgin Mary.

There appears to have been a rood screen thrown between the two western piers of the crossing.
A rood loft may have surmounted it.
Against this screen was placed the altar of St Nicholas, the parochial altar of the city.
The citizens demanded the right of entrance by day or night to what was after all their altar.
There were also crowds of strangers passing through the city.
The friction broke out as a riot in 1327 after which the strong stone screens and doors which wall off the eastern end of the church from the nave were built.
The priory itself was walled off from the town at this period.
An oratory was established in angulo navis ("in the corner of the nave") for the reserved sacrament; it is not clear which corner was being referred to, but Dr Palmer argues that the buttress against the north-west tower pier is the most likely setting.
He notes the arch filled in with rubble on
Probably from about 1190, Gilbert de Glanville (bishop 1185–1214) commenced the rebuilding of the east end and the replacement on the monastic buildings. The north quire transept may have been sufficiently advanced to allow the burial of St William of Perth in 1201, alternatively the coffin may have lain in the north quire aisle until the transept was ready. It was then looted in 1215 by the forces of King John during siege of Rochester Castle. Edmund de Hadenham recounts that there was not a pyx left "in which the body of the Lord might rest upon the altar". However, by 1227, the quire was again in use when the monks made their solemn entry into it. The cathedral was rededicated in 1240 by Richard Wendene (also known as Richard de Wendover) who had been translated from Bangor.
The shrines of Ss Paulinus and William of Perth, along with the relics of St Ithamar, drew pilgrims to the cathedral. Their offerings were so great that both the work mentioned above and the ensuing work could be funded.
Unlike the abbeys of the period (which were led by an abbot) the monastic cathedrals were priories ruled over by a prior with further support from the bishop. Rochester and Carlisle (the other impoverished see) were unusual in securing the promotion of a number of monks to be bishop. Seven bishops of Rochester were originally regular monks between 1215 and the Dissolution. A consequence of the monastic attachment was a lack of patronage at the bishop's disposal. By the early 16th century only 4% of the bishop's patronage came from non-parochial sources. The bishop was therefore chronically limited in funds to spend on the non-monastic part of the cathedral.
The next phase of the development was begun by Richard de Eastgate, the sacrist. The two eastern bays of the nave were cleared and the four large piers to support the tower were built. The north nave transept was then constructed. The work was nearly completed by Thomas de Mepeham who became sacrist in 1255. Not long after the south transept was completed and the two bays of the nave nearest the crossing rebuilt to their current form. The intention seems to have been to rebuild the whole nave, but probably lack of funds saved the late Norman work.
The cathedral was desecrated in 1264 by the troops of Simon de Montfort, during sieges of the city and castle. It is recorded that armed knights rode into the church and dragged away some refugees. Gold and silver were stolen and documents destroyed. Some of the monastic buildings were turned into stables. Just over a year later De Montfort fell at the Battle of Evesham to the forces of Edward I. Later, in 1300, Edward passed through Rochester on his way to Canterbury and is recorded as having given seven shillings (35p) at the shrine of St William, and the same again the following day. During his return he again visited the cathedral and gave a further seven shillings at each of the shrines of Ss Paulinus and Ithamar.
The new century saw the completion of the new Decorated work with the original Norman architecture. The rebuilding of the nave being finally abandoned. Around 1320 the south transept was altered to accommodate the altar of the Virgin Mary.
There appears to have been a rood screen thrown between the two western piers of the crossing. A rood loft may have surmounted it. Against this screen was placed the altar of St Nicholas, the parochial altar of the city. The citizens demanded the right of entrance by day or night to what was after all their altar. There were also crowds of strangers passing through the city. The friction broke out as a riot in 1327 after which the strong stone screens and doors which wall off the eastern end of the church from the nave were built. The priory itself was walled off from the town at this period. An oratory was established in angulo navis ("in the corner of the nave") for the reserved sacrament; it is not clear which corner was being referred to, but Dr Palmer argues that the buttress against the north-west tower pier is the most likely setting. He notes the arch filled in with rubble on 
Rochester Cathedral