St. Martin's was one of the parishes whose delegates at the Diocesan Synod in June, 2002, protested the synod's decision of to ask for a blessing of same sex unions. The diocese that summer began withholding their assessment to the Diocese. The rector, the Rev. Timothy Cooke, resigned as of the end of January, 2004, and left the diocese.

Shortly afterwards the Bishop met with the wardens and, with their agreement, appointed a temporary priest- in-charge, the Rev. Don Willis, to provide stability and care while the parish could begin a search for an new through the diocesan process. The usual practice is for a parish committee to write a description of the parish and their expectations for a priest; a diocesan committee (elected annually) and the bishop prepare a short list of candidate from those who apply for the position; the parish chooses from the short list; and the bishop appoints the priest rector of the parish.

Despite the urging of the bishop to get on with the task of finding a new priest, the parish seemed unable to proceed. The parish's governing group of wardens and trustees, and the advisory Church Committee, reflecting the membership as a whole, were split. Some wished to work with a group of dissenting parishes; others wanted to retain ties with the diocese.

In March, 2003, Bishop Terry Buckle of the Diocese of Yukon offered to provide alternate episcopal oversight to dissenting parishes, an act that the diocese and the chief bishop in British Columbia, Archbishop David Crawley, considered irregular and contrary to canon (church) law.

In May, 2003, the leaders of the parish decided to ask the parish congregation (the Vestry) whether they wanted to accept Bishop Buckle's offer. The Church Committee decided that a 60 per cent vote would be required (reduced from two-thirds). On May 25 the vote failed by a slim margin, with 59.73 per cent in favour. Proponents of disassociation from the diocese persuaded the Church Committee to “round up” the vote to 60 per cent and accept Bishop Buckle's offer. (Subsequently in November, 2003, at the urging of the Canadian House of Bishops, Bishop Buckle withdrew from all interference in the Diocese of New Westminster.)

The parish continued in some turmoil over the summer. Finally, on September 7, Archdeacon Ron Harrison announced at Sunday morning services that the Bishop Michael Ingham had invoked diocesan Canon 15, which enables him to reorganize a parish “experiencing difficulties or a crisis which in the opinion of the bishop affects the orderly management and operation of the parish.” The bishop was dismissing the elected wardens, trustees, and Church Committee, and in their place appointed three Bishop's Wardens. (Two of the three Bishop's Wardens, Lindsey Buchanan and Steve Priest, had previously been elected as wardens; Bishop's Warden was Joe Arduini was new. All are members of the parish.)

In the statement read to the parish, the bishop wrote the following:

I have been aware now for several months of the conscientious disagreement many of you have had with a recent decision of our Diocesan Synod. As I have continually made very clear, no priest or parish is being asked to offer a ceremony or service of blessing which in conscience they cannot. Your commitment to the traditional teaching and worship of the Anglican Church is respected and honoured by all of us in the Diocese of New Westminster.

At the same time, Christian tradition includes respect for order. Faith and order are both deeply cherished among Anglicans. In the last few months I have become profoundly concerned about the challenge to the order of the church which is under way at St. Martin's. I believe this is disrupting what the Prayer Book calls our "godly quietness" and diminishing our mission within the wider community…

My hope is that stability and normalcy will return very soon and that we can quickly begin to seek your new Incumbent. Please accept my assurance that your commitment to the traditional teaching of our church is in no way being abrogated. Rather, I am insisting that the historic structures of our church be respected.

On January 11, 2004, the Bishop's Wardens announced that the parish was able to begin work on a process leading to appointment of a permanent priest. They also announced that the parish was recommencing its parish assessment payments as full and active members of the Diocese of New Westminster.

In February two former wardens of the parish, James Burns and Christopher Vondette, announced they intended to go to the Supreme Court of British Columbia seeking reinstatement. Chancellor George Cadman, the chief legal officer of the diocese, said the diocese would oppose the move. He said that local church elections will be held again once the bishop is satisfied the parish is no longer embroiled in dissention. The legal case would not change that situation, but regretted it could use up church money that would otherwise go for outreach ministry in the Lower Mainland.