[5] After Hooker was forced to flee to the Netherlands, Eliot emigrated to Boston, Massachusetts, arranging passage as chaplain on the ship Lyon and arriving on 3 November 1631.

Eliot disapproved of Hutchinson's views and actions, and was one of the two ministers representing Roxbury in the proceedings which led to her excommunication and exile.

By 1663, Marmaduke and Green had printed 1,180 volumes of the Old and New Testaments translated from English to the Massachusett Indian language.

[14][15][16] The first time Eliot attempted to preach to Indians (led by Cutshamekin) in 1646 at Dorchester Mills,[17] he failed and said that they, "gave no heed unto it, but were weary and despised what I said.

"[10] The second time he preached to the Indians was at the wigwam of Waban near Watertown Mill which was later called Nonantum, now Newton, MA.

[10] This was important because the settlements of "praying Indians" could be provided with other preachers and teachers to continue the work John Eliot started.

As a missionary, Eliot strove to consolidate the Algonquian Indians in planned towns, thereby encouraging them to recreate a Christian society.

Other praying Indian towns included: Littleton (Nashoba), Lowell (Wamesit, initially incorporated as part of Chelmsford), Grafton (Hassanamessit), Marlborough (Okommakamesit), a portion of Hopkinton that is now in the Town of Ashland (Makunkokoag), Canton (Punkapoag), and Mendon-Uxbridge (Wacentug).

Eliot's better intentions can be seen in his involvement in the legal case, The Town of Dedham v. The Indians of Natick, which concerned a boundary dispute.

[22] Praying Indian towns were also established by other missionaries, including the Presbyterian Samson Occom, himself of Mohegan descent.

In 1661 the General Court forced Eliot to issue a public retraction and apology, banned the book and ordered all copies destroyed.

John Eliot married Hanna Mumford in September 1632, the first entry in the "Marages of the Inhabitants of Roxbury" record.

[30] William Carey considered Eliot alongside the Apostle Paul and David Brainerd (1718–1747) as "canonized heroes" and "enkindlers" in his groundbreaking An Enquiry Into the Obligation of Christians to Use Means for the Conversion of the Heathen (1792).

[31] In 1689, he donated 75 acres (30 ha) of land to support the Eliot School in what was then Roxbury's Jamaica Plain district and now is a historic Boston neighborhood.

Eliot's donation required the school (renamed in his honor) to accept both Black and Native American students without prejudice, which was very unusual at the time.

Present-day Newton is the site of Eliot’s first sermons to the Natives, which took place in Waban’s wigwam among what would be later called the Nonantum Indian community starting on October 28, 1646.

A group of time travelers bring a book about the world they come from that allows Eliot to read about how much of his works were undone by his fellow colonists, he then sets out to alter his missionary efforts in a manner that will prevent Native American converts from being vulnerable to the treachery they faced in the old timeline.