When the civil war broke out, he was dubious how to steer. He took the protestation which the parliament required, to defend the king's person, honour, and authority, the power and privileges of parliaments, the liberties of the subject, and the protestant religion, against the common enemy. And he joined with the magistrates of Kidderminster, in offering the same protestation to the people. A little after, the king's Declarations were read there in the market-place, and the commission of array was set on foot; upon which the rabble grew so riotous and furious, that he was advised to withdraw awhile from home. He retired to Worcester, and so to Gloucester, where he first met with the anabaptists; and after a month's absence he returned home, lest his absence should be interpreted either as the effect of fear on the account of some guilt, or as signifying his being against the king. At his return he found the drunken rabble very boisterous; and their common cry was this, We shall take an order with the puritans ere long. He did not think himself in safety if he stayed at home, and so he withdrew again. He preached at Alcester, on that Lord's day that was the day of Edge-hill fight; and was informed while he was preaching, by the noise of the cannon, that the armies were engaged. And the next day he went into the field of battle.
The soldiers on one side or the other still passing to and fro, and being ready to make a prey of whatsoever came before them, he determined to go to Coventry, and stay there till one side or other had got the victory, and the war was ended, which it was then thought would be in a very little time. The committee and governor of that city desired him to stay with them and lodge in the governor's house, and preach to the soldiers; which offer he readily accepted. He continued there a year, preaching once a week to the soldiers, and once on the Lord's day to the people, having nothing but his diet for his pains. Here he had the society of about thirty worthy ministers, who fled to the same place for safety, and among the rest, of Mr. Vines and Mr. Anthony Burgess. When his year expired, he found the war so far from being ended, that it had dispersed itself into almost all the land. He determined therefore to continue there another year; and in that time preached over all the controversies against the anabaptists, and against the separatists, and so kept the garrison sound. After the fight at Naseby, (not far from Coventry,) he went into the army to visit some of his old intimate friends. He stayed there a night, and got such intelligence as to their state as amazed him. He found plotting heads were designing to subvert both church and state. The sectaries were like to carry all before them, and were resolved to take down not only bishops, liturgies, and ceremonies, but all that did withstand them. This made him lament that the ministers had left the army, as they generally did, after Edge-hill fight. It made him also repent his refusing of Cromwell's invitation to be the pastor of his troop, when he first raised it; by which means he would have had an opportunity of dealing freely with those that afterwards headed much of the army, and were the forwardest in all the public changes. But he was told that it was not even yet too late to do service, if he would come into the army; and was invited by Colonel Whalley to be chaplain to his regiment. He returned to Coventry, and consulted the ministers that were there, and with their advice, (in order to do what in him lay to prevent the mischief that was threatened by the prevailing temper of the army,) he accepted the invitation.
When he came thither, Cromwell welcomed him but coldly. He set himself from day to day to discourse the officers and soldiers out of their mistakes, both religious and political. He found a few fiery, self-conceited men among them made all the noise and bustle, and carried about the rest as they pleased. Some of these became the laughing-stock of the soldiers before he left them. He marched with the army westward, and was at the taking of Bridgwater, and the siege of Bristol, and Sherborne Castle, and Exeter. He was also with Colonel Whalley before Banbury Castle, and at the siege of Worcester. He had full employment in opposing the sectaries in all places: and particularly he had at one place a dispute with them of a whole day's continuance. And by what success he met with, he found reason to apprehend, that if there had but been a competent number of ministers, each doing their part, the whole plot of the furious party might have been broken, and king, parliament, and religion preserved. But he was separated from the army by great weakness, occasioned by the loss of a gallon of blood at the nose; upon which, retiring to Sir Thomas Rouse's, he was taken up with daily medicines to prevent a dropsy, and was in continual expectation of death.