The crash came on 23rd December 1940 when the parish was virtually destroyed in one night. The church survived but, with roof tiles blasted away, it was some months before Masses could resume in the patched-up Lady Chapel. Now began the valiant years for Fr Coles. Alone and amid the ruins of his parish he faithfully continued his ministry, in great hardship, steadfastly refusing to abandon his beloved St Agatha's. Despite his advancing years and being almost blind he continued the round of daily Mass, assisted by devoted servers. For the next fourteen years he lived in the choir vestry keeping watch over God's House. In 1954, worn and frail, Fr Coles suffered a severe stroke and was forced to leave his beloved church. The end was now at hand.

The Anglican diocese of Portsmouth abandoned the church to its fate, closing it in the same year that Fr Coles left. A year later, stripped like a carcass by vultures, the church was compulsorily purchased for use as a naval store. A glorious chapter had come to an end but the book had yet to close.

A floor was inserted, just below the level of the capitals and the whole building was divided into storage pens. Lorries backed in and out, cobwebs formed and store-men talked of a ghostly figure which seemed to haunt the church.