

An exception to the cross-less flags would be on Castle Island. The commissioners ordered that the cross-less banners be used. It ordered that commissioners be made to standardize military banners. In 1636 the General Court made another ruling concerning banners in the colony. The controversy remained, and some units refused to train for militia duty under a flag bearing St George's Cross. The General Court did rule however that the defaced flag was not to be used in any official capacity. The Council of Assistants reviewed the matter and the case was dismissed against Endicott and Davenport. Browne brought the matter before the Great and General Court of Massachusetts Bay. A freeman of the colony named Richard Browne was disturbed by this and feared it could signal to authorities in England that the colonists were rebelling. Richard Davenport of Watertown, the bearer of the flag was to be the one to remove it. John Endicott who was inspired by Williams and then a member of the Council of Assistants ordered that the cross be cut out from flags in the colony. Roger Williams, a prominent religious leader then based in Salem declared the symbol counter to the Reformation and a vestige of papal authority over the king. Reverend William Hubbard was an early opponent of the use of the cross on New England banners. George was seen by many Puritans as a symbol of the Papacy and a symbol of religious heresy. The use of the red ensign with the flag of England in the canton was controversial in the region. Other symbols that can be seen as derived from Oliver Cromwell’s New Model Army are hearts ( Worcester, Massachusetts), and the motif of an armored divine arm still exists in Massachusetts today as a component of the state's official seal as the crest, and well as the symbol of the Massachusetts National Guard (the Massachusetts National Guard contains the oldest units in the United States Army and is a direct successor/continuation of these early militias). The anchor, a symbol of hope and providence, was common in Rhode Island and is still a symbol of the state today. Grapevines were prominent in the Connecticut and Saybrook colonies, and remain on the current state of Connecticut's flag and state seal. Other Puritan and religious symbols such as anchors, grapevines, oak trees were also flown. This was a symbol also seen in the English Civil War and was supposed to symbolize divine justice being carried out in defense of true believers. These banners depicted an armored arm reaching from the heavens holding a sword.

Examples of such flags are the “Three County Troop” flag or the militia flag, known today as the Bedford Flag. Around 1652 new cavalry regiments were created. As Puritan militias grew in size, more units necessitated additional banners. One of the Newburyport green ensigns depicted mailed hands arranged in a circle, which is a symbol of the divine in Puritan iconography.

Influenced by the Commonwealth of England and the parliamentary forces of the English Civil War, some flags in New England bore similar motifs and symbols. Puritan influence can be seen on some company and settlement banners as well. Greens ensigns are associated with Newburyport and red ensigns were flown in the Massachusetts Bay Colony and Saybrook Colony for some units. These differences are evident in colonial flags in the New England Colonies. A company with a green ensign could be referred to as the “green regiment”, a blue ensign referred to as the “blue regiment”, and so on. Each regiment also had a particular color associated with it. Defacements could include circles, flames, or any distinguishing mark. Colonial militias were relatively limited in size compared to the larger forces in Britain and so these changes never exceeded the defacements found on company sized regiments. As with the military on the British Isles, the colonists' military banners corresponded more to an individual commander rather than an emblem of a national force. This included style, color of the ensigns’ field, and any defacements. The designs of the flags changed by location. The same issues with naval flags were also found here. In North America, the colonists relied for a large part on their own militias for security and defense. The lack of uniformity of the red ensign existed with land forces of the British Empire as well. These designs sometimes greatly varied by location, the type of vessel flying the flag, the rank of the commanding officer of the vessel, or the position of the vessel within the royal fleet. What was consistent was all the flags featured the Cross of St. Although it was an official flag of Great Britain there was no official or standardized design of the banner. The red ensign was first used in 1625, with merchant vessels being granted its usage by 1663. The origin of the New England flag lay with the Red Ensign of the Royal Navy.
