He sued the church on employment discrimination grounds. However, a tribunal upheld his dismissal, saying that being a Church of England chaplain meant that Pemberton had to uphold that church's views on marriage. The tribunal also said that the Equality Act in England and Wales allowed for religious exemptions to laws that protect people from being fired because of their sexual orientation. The dismissal was upheld on appeal by the Court of Appeal in 2018.
By 2005, after teaching theology in the Democratic Republic of Congo (DRC), he became an honorary canon of Boga-Zaire in the DRC. He was also an honorary canon of Ely in Cambridgeshire while he worked as team rector of 13 parishes in West Cambridgeshire.[2]
In April 2014, Pemberton married his partner Laurence Cunnington;[4] Pemberton met Cunnington on a support website for gay fathers in 2008 and both had been previously married to women for several decades; Pemberton and his former wife had five children.[2][5] The marriage occurred despite an official ban on same-sex marriages from the Church of England's House of Bishops in February 2014,[6] who instead allowed civil partnerships between members of the same gender, within a celibate relationship.[7] The Marriage (Same Sex Couples) Act 2013 meant that religious institutions which do not agree with same-sex marriage—such as the Church of England, which defines marriage as between one man and one woman in its canon law—did not have to perform same-sex marriage ceremonies. These exemptions came following extensive lobbying by conservative Anglicans.[2]
The Archbishop of York (whose ecclesiastical jurisdiction includes Southwell), John Sentamu, an opponent of same-sex marriage, opposed Pemberton's move. Following consultation with Sentamu, Bishop Richard Inwood refused Pemberton permission to officiate (PTO) in the Diocese of Southwell and Nottingham.[7] A PTO is only rarely revoked, usually only when the law is broken.[2] As a result, the NHS refused his chaplaincy at King's Mill Hospital, though he still worked for the Lincolnshire NHS trust.[8]
In response, Pemberton threatened legal action against the church.[7] This led to a tribunal. Pemberton approached three barristers and the church hired the law firm Herbert Smith Freehills. At the tribunal, a registrar of the Diocese of London, a solicitor for Justin Welby, the Archbishop of Canterbury, a legal secretary from the church's general synod, and a legal representative of the church's pensions board were present, among others. Tom Linden QC, representing the church, took an aggressive line against Pemberton, calling him "errant", "not in good standing" and heavily chastising him for crying over the revocation of his PTO.[2]
The tribunal upheld the church's position, saying that supporting the church's position on same-sex marriage was a requirement of being a Church of England chaplain, and that the act allows religious groups exemptions in anti-employment discrimination law.[9] This judgement was criticised by the LGBT rights activist Peter Tatchell[10] and the LGBT rights charity Stonewall.[11]
Precisely five years after his marriage, Equal, the Campaign for Equal Marriage in the Church of England, was founded to end bans on same-sex marriages in churches and to allow clergy to marry people of the same sex.[16]