Witch trials When Phips arrived, rumors of witchcraft were running rampant, especially in
Salem. Phips immediately appointed Stoughton to head a special tribunal to deal with accusations of witchcraft, and in June appointed him chief justice of the colonial courts, a post he would hold for the rest of his life. In the now-notorious
Salem Witch Trials, Stoughton acted as both chief judge and prosecutor. 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. Many convictions were made because Stoughton permitted the use of
spectral evidence, the idea that a demonic vision could only take on the shape or appearance of someone who had made some sort of devilish pact or engaged in witchcraft. Although
Cotton Mather argued that this type of evidence was acceptable when making accusations, some judges expressed reservations about its use in judicial proceedings. Stoughton, however, was convinced of its acceptability, and may have influenced other judges to this view. The special court stopped sitting in September 1692. This turn of events angered Stoughton, and he briefly left the bench in protest.
Acting governor Stoughton was also involved in overseeing the colonial response to
King William's War, which had broken out in 1689. 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. Phips was frequently in Maine overseeing the construction of defenses there, leaving Stoughton to oversee affairs in Boston. 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. In early 1694 Phips was recalled to London, to answer charges of misconduct. He delayed his departure until November, at which time Stoughton took over as acting governor. Phips died in London in early 1695, before the charges against him were heard. Stoughton viewed himself as a caretaker, holding the government until the crown appointed a new governor. As a consequence, he gave the provincial assembly a significant degree of autonomy, which, once established, complicated the relationship the assembly had with later governors. He also took relatively few active steps to implement colonial policies, and only did the minimum needed to follow instructions from London. A commentator in the colonial office observed that he was a "good scholar", but that he was "not suited to enforce the
Navigation Act". In 1695 Stoughton protested the actions of French
privateers operating from
Acadia, who were wreaking havoc in the New England fishing and merchant fleets. In an attempt to counter this activity, he authorized
Benjamin Church to organize a raid against Acadia. While Church was recruiting men for the expedition, New France's governor,
the comte de Frontenac, organized an expedition to target
the English fort at Pemaquid, Maine. Church had still not departed in August 1696 when he learned that the fort
had been taken and destroyed. 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. The failure of these expeditions highlighted the inadequacies of the provincial forces, and the Massachusetts assembly appealed to London for aid. Peace between France and England was achieved with the
Treaty of Ryswick in 1697, but it did not resolve any issues concerning the
Abenakis to the north. As a result, there continued to be tension on the frontier, and disputes over fishing grounds and the use of Acadian territory by New Englanders for drying fish continued. 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 appealed to London for diplomatic assistance, which had some success in reducing tensions. Stoughton served as acting governor until 1699, while still also serving as chief justice. He remained lieutenant governor during the brief tenure of
the Earl of Bellomont as governor, and again became acting governor on the latter's departure in 1700. He was by then in poor health, and accomplished little of note in his final year.
Harvard and the Brattle Street Church , 1859 The corporate existence of
Harvard College had been thrown into turmoil by the recission of the colonial charter in 1684, upon which the Harvard charter depended. In 1692 the provincial assembly passed a law enacting a new charter for the college, but the Board of Trade vetoed this law in 1696, again throwing the college's existence into jeopardy. Stoughton, then acting governor, made temporary arrangements for the college's governance while the assembly worked to craft a new charter. Ultimately, Harvard's charter problems would not be solved until 1707, when its 1650 charter was revived. Religious and political differences between factions of directors at Harvard boiled into the open during the late 1690s.
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. 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. Stoughton and a number of other high-profile religious and political figures in the colony stepped in to resolve the dispute. The peace was so successfully brokered that the elder Mather took part in the new church's dedicatory services. ==Family and legacy==