While the soldiers were expecting his orders to begin their exercise, they saw him take the banner in one hand, holding his drawn sword in the other.

Probably he addressed them in a speech, and explained how horrible a thing it was, that men, who had fled from Popish idolatry into the wilderness, should be compelled to fight under its symbols here.

Perhaps he concluded his address somewhat in the following style.
"And now, fellow soldiers, you see this old banner of England.

Some of you, I doubt not, may think it treason for a man to lay violent hands upon it.

But whether or no it be treason to man, I have good assurance in my conscience that it is no treason to God.