The Commission died with the king, and Laud, becoming bishop, persuaded Charles to issue a new one. This time a handsome sum was collected, and work was commenced. As regards the exterior, the nave and west sides of the two transepts were cased throughout, and some repairs made to the east end.[29] The chief alteration in the interior was the adornment and restoration of the choir screen, at the expense of Sir Paul Pindar, and with the laudable object of putting an end to desecration. Inigo Jones added a noble classical portico to the West End as a successor to Paul's Walk. We forgive the lack of harmony with the Norman nave, when we recall the truly religious motive.

But evil days for the cathedral were approaching. In the House of Commons (February 11, 1629), Oliver Cromwell, Member for Huntingdon town, made his maiden speech in a Grand Committee on Religion. He complained that Dr. Alablaster had preached flat Popery at Paul's Cross, and that the Doctor's bishop, Neile of Winchester, would not have it otherwise.[30] Alablaster was High Church, and the Third Parliament of Charles was not.

The Civil War.—The outbreak of the Civil War put an end to the Commission, and the moneys were confiscated.[31] The Long Parliament acquired the supremacy in the City, and from 1643 Inigo Jones ceased to act as surveyor, dying before the Restoration. The whole staff was expelled, and their revenues sequestrated; and Dr. Cornelius Burgess was appointed preacher, some of the more eastern bays of the choir being walled in by a brick partition as his chapel or conventicle. The chief fault to be found with Burgess is that he was out of place in a cathedral, otherwise there is much to be said in his favour. Even in those times, when religious fanaticism went mad, he behaved with discretion, and courageously headed the petition of London ministers against the execution of the king. Hugh Peters figures in the crypt, and other parts were assigned as meeting-houses. It is better to pass over as quickly as may be the behaviour of the soldiery and populace. "Paul's Cathedral," says Carlyle, "is now a Horseguard; horses stamp in the Canons' stalls there [but the choir was mainly reserved for Burgess and his sermons], and Paul's Cross itself, as smacking of Popery ... was swept altogether away, and its leaden roof melted into bullets, or mixed with tin for culinary pewter."[32] Its very name, the Cross, was against it; and thus fell, never to be restored, the most famous pulpit in England, which through successive generations had been part and parcel of English history. Carlyle also tell us that Trooper Lockyer, of Whalley's Horse, "of excellent parts and much beloved," was shot in the churchyard for mutiny, "amid the tears of men and women."[33]

Monuments which had escaped earlier vandals were now defaced and destroyed; the scaffolding was seized; part of the roof on the south side fell in, and the lead was used for water-pipes. The new portico was hacked about and turned into stalls for wares, and, in a word, Inigo Jones' work more than undone. Other doings of the soldiery are unfit for publication.[34]

The Restoration.—Juxon was translated to Canterbury, and the munificent and much-abused Gilbert Sheldon received London, only in turn to succeed Juxon again three years later. At the beginning of the Civil War the deanery had become vacant, and Richard Steward designated for the vacancy. It was an empty appointment, and was afterwards changed for another of a like kind, and Matthew Nicolas became nominally dean. This preferment took actual effect from the summer of 1660, when Nicolas was installed dean and prebendary of Caddington Major, such of the other dignitaries as survived resuming their stalls, and vacancies were filled up. Another bay was added to the Burgess conventicle, and the cathedral services were resumed. But the sad condition of the fabric called for action, and in 1663 another Commission was appointed, and Christopher Wren appointed surveyor. Taking example from his uncle's cathedral at Ely, he suggested an enlargement of the area at the junction of the four members of the cross, and subscriptions were raised.

The Plague.—There is a gap in the subscription list after March, 1665: the pestilence was already at work. As the summer advanced its ravages were intensified; and the City, fortunate in escaping earlier attacks, suffered so severely that the pest-houses proved insufficient; and Harrison Ainsworth is responsible for a story which may probably be depended on in its main outlines. The Lord Mayor and City authorities, in conjunction with the College of Physicians, obtained the consent of Dean Sancroft (the second from Nicolas) and his chapter for the conversion of the cathedral into a lazar-house; and a meeting was held in the Chapter House, at which the Primate Sheldon was present. Sheldon employed himself, co-operating with the Lord Mayor, in making provision for the victims. "Chapels and shrines," says Ainsworth, "formerly adorned with rich sculptures and costly ornaments, but stripped of them at times when they were looked upon as idolatrous and profane, were now occupied by nurses, chirurgeons and their attendants; while every niche and corner was filled with surgical instruments, phials, drugs, poultices, foul rags and linen."[35] After its chequered career, Old St. Paul's was destined to be used last of all as a hospital.

The Fire.—The house and Navy office of Samuel Pepys were in Seething Lane, Crutched Friars, near where Fenchurch Street Station now is. About three in the morning of Sunday, September 2, 1666, Samuel and his wife were called by their servant Jane, who told them of a fire visible in the south-west towards London Bridge. After looking out, not thinking it a great matter, the couple returned to bed; but getting up at seven Pepys heard a far worse account, and instead of attending morning service went to the Tower, and called on his neighbour Sir John Robinson, the Lieutenant. Robinson told him that the house of Faryner, baker to the king, in Pudding Lane had just caught fire, that Fish Street was in flames, and the church of St. Magnus destroyed. These were near the north end of London Bridge, as the Monument and St. Magnus both remind us.

The origin of the Fire Pepys learnt later (February 24, 1667). Faryner's people had occasion to light a candle at midnight; they went as usual into their bakehouse to light it, but as the fire had gone out, had to seek elsewhere. This striking a light in an unusual place by Faryner, his son and daughter, is asserted to have been, somehow and all unknown to them, the origin of the Fire. "Which is," says Pepys, "a strange thing, that so horrid an effect should have so mean and uncertain a beginning." About two in the morning, when the family were upstairs and asleep again, the choking sensation of smoke woke them up, just in time to escape and tell the tale.