During this short interval of public liberty, those ministers that were not for episcopacy, Liturgy, and ceremonies, were represented as seditious, and loaded with calumnies and reproaches. Many of them were imprisoned, together with some sober gentlemen, in several counties, under pretence of their plotting against the government. Particularly a plot was hatched in Worcestershire. A packet was pretended to be found under a hedge, left there by a Scotch pedlar. In it there were letters from several ministers; and among the rest, one from Mr. Baxter; intimating, that he had provided a considerable body of men well armed, which should be ready against the time appointed. And indeed where men were taken up and imprisoned in distant counties, it was said to be for Baxter's plot. The noise of these plots in so many counties, paved the way for the Act of Uniformity, which gave all the ministers who could not conform no longer time than till Bartholomew day, 1662, when they were all cast out. Mr. Baxter preached his last sermon in public on the 25th of May before, at Black-friars. The reason of his forbearing preaching so soon, was partly because the lawyers did interpret a doubtful clause in the Act of Uniformity, as putting an end to the liberty of lecturers at that time; and partly because he would let all the ministers in the nation understand in time what his intentions were, lest any might be influenced to a compliance, upon a supposition that he intended to conform.
After this, if the ejected ministers did but meet to pray together it was a seditious conventicle. Dr. Bates and Mr. Baxter were desired to pray at a friend's house, for his wife that was sick of a fever, and had they been there they had been apprehended by a warrant from two justices. Finding therefore his public service at an end, he retired to Acton, in Middlesex; where he went every Lord's day to the public church, and spent the rest of the day with his family, and a few poor neighbours that came in to him. In the time of the plague, in 1665, he went to Mr. Hampden's, in Buckinghamshire; and returned back again to Acton when it was over. He stayed there as long as the Act against Conventicles was in force, and when it was expired, he had so many came to hear him, that he wanted room. Hereupon he by a warrant of two justices, was committed to New-Prison gaol for six months. But he got a Habeas Corpus, and was released; and removed to Totteridge, near Barnet. While he was there, Duke Lauderdale going into Scotland, signified to him a purpose there was of taking off the oath of canonical obedience, and all impositions of conformity, save only that it should be necessary to sit in presbyteries and synods with the bishops and moderators; and that he had the king's consent to offer him what place in Scotland he would choose, either a church, or a college, or a bishopric. But he excused himself from his weakness and indisposition, and the circumstances of his family.
After the Indulgence, in 1672, he returned to his preaching in the city. He was one of the Tuesday lecturers at Pinner's Hall; and had a Friday lecture at Fetter Lane; but on Lord's days he only preached occasionally. He afterwards preached in St. James's Market house, where on July 5, 1674, they had a marvellous deliverance. For a main beam, that had before been considerably weakened by the weight of the people, gave such cracks, that three several times they ran out of the room, concluding it was falling. The next day taking up the boards they found that two rends in the beam were so great, that it was a wonder of Providence that the floor had not fallen, and the roof with it, to the destruction of multitudes. He was afterwards apprehended as he was preaching his Thursday lecture at Mr. Turner's; but soon released, because the warrant was not signed by a city justice, as it should have been, when he was apprehended for preaching in the city. In 1676, by the assistance of his friends, he built a new meeting-house in Oxenden Street, and when he had preached there but once, a resolution was taken to surprise him the next time, and to send him for six months to gaol upon the Oxford Act. But he being out of town, Mr. Seddon, a Derbyshire minister, preaching for him, was sent to the Gate-house in his room, though the warrant did not suit him; and he was forced to continue there three months, till he had a Habeas Corpus. He afterwards built another meeting-house in St. Martin's parish, but was forcibly kept out of it by constables and officers: and thereupon Mr. Wadsworth, in Southwark, dying, he upon the invitation of his people preached to them many months in peace. And when Dr. Lloyd succeeded Dr. Lamplugh, in St. Martin's parish, he offered him his chapel, in Oxenden Street, for public worship, and accepted it.[3]