He was one of the province's major landowners, partnering with Joseph Dudley and other powerful figures in land purchases, and it was for him that the town of Stoughton, Massachusetts was named.

"[3] England was at the time under Puritan Commonwealth Rule, although 1653 was the year Oliver Cromwell dissolved Parliament, beginning The Protectorate.

Dudley and Stoughton used their political positions to ensure that the titles to lands they were interested in were judicially cleared, a practice that also benefited their friends, relatives, and other business partners.

"[11] This was particularly obvious when Stoughton and Dudley were part of a venture to acquire 1 million acres (4,000 km2) of land in the Merrimack River valley.

[14] When Andros was arrested in April 1689 in a bloodless uprising inspired by the 1688 Glorious Revolution in England, Stoughton was one of the signatories to the declaration of the revolt's ringleaders.

He was particularly harsh on some of the defendants, sending the jury deliberating in the case of Rebecca Nurse back to reconsider its not guilty verdict; after doing so, she was convicted.

Although Cotton Mather argued that this type of evidence was acceptable when making accusations, some judges expressed reservations about its use in judicial proceedings.

[24] In November and December 1692 Governor Phips oversaw a reorganization of the colony's courts to bring them into conformance with English practice.

The new courts, with Stoughton still sitting as chief justice, began to handle the witchcraft cases in 1693, but were under specific instructions from Phips to disregard spectral evidence.

As a result, a significant number of cases were dismissed due to a lack of evidence, and Phips vacated the few convictions that were made.

[20] Historian Cedric Cowing suggests that Stoughton's acceptance of spectral evidence was based partly in a need he saw to reassert Puritan authority in the province.

Massachusetts Bay (which included the area now known as Maine) was in the forefront of the war with New France, and its northern frontier communities suffered significantly from French and Indian raids.

[27] During one such absence, for example, Stoughton was responsible for raising a small force of militia intended to help protect neighboring New Hampshire, which was similarly being devastated by raids.

[30] In 1695 Stoughton protested the actions of French privateers operating from Acadia, who were wreaking havoc in the New England fishing and merchant fleets.

[32] The instructions Stoughton issued to Church were somewhat vague, and he did little more than raid Beaubassin at the top of the Bay of Fundy before returning to Boston.

Before Church's return Stoughton organized a second, smaller expedition that unsuccessfully besieged Fort Nashwaak on the Saint John River.

Stoughton and Acadian Governor Joseph Robineau de Villebon exchanged complaints and threats in 1698 over the issue, with Villebon issuing largely empty threats (he lacked the needed resources to execute them) to seize Massachusetts ships and property left in Acadian territory.

Stoughton, then acting governor, made temporary arrangements for the college's governance while the assembly worked to craft a new charter.

Increase Mather, then the president of Harvard, was theologically conservative, while a number of the directors had adopted moderate views, and in these years they began a struggle for control of the college.

[40] This split eventually led to the founding in 1698 of Boston's Brattle Street Church, which issued a manifesto explicitly distancing itself from some of the more extreme Puritan practices advocated by Mather and his son, Cotton.

[43] Stoughton was given the then-prestigious Green Dragon Tavern for his social status, one of Boston's most significant architectural and historical landmarks c. 1676.