Covenant of Grace
The New England Puritans viewed a covenant as a contract.  Unlike a promise, it was legally binding.  They preached that they entered into a covenant with God through their ancestor Abraham. This Covenant of Grace, replacing the Covenant of Works entered into with Adam, guaranteed the New Englanders that God would not do anything unexpected, outside the boundaries of the agreement.  In turn they served God according to the Scriptures.  What this covenant meant, as an agreement entered into freely and voluntarily on the part of both parties, is that God, who is omnipotent, can go anywhere and is capable of anything, has bound himself to the law (Miller, Seventeenth, pgs. 375-380). The Puritan universe was fixed and unchanging, created and completely known by God (Miller, Seventeenth, pg.365-366).  This gave the Puritans the assurance that God would not arbitrarily afflict them. 

"In the Covenant of workes, a man is left to himselfe, to stand by his own strength; But in the Covenant of Grace, God undertakes for us, to keep us through faith" 
(Miller, Seventeenth, pg. 377).

It was necessary to reconcile the contradiction between their doctrine of the elect, assurance of God's grace as His chosen people, and Old Testament evidence that God allowed his chosen people to suffer (see Job). The covenant, sealed in the sacrament of baptism, implied, "a league between God and man" (Miller, Seventeenth, pg. 502). The Covenant of Grace promised Abraham and his descendants salvation and assurance for their own sake, regardless of the sins they committed. God saw humanity as imperfect, yet he loved them anyway, as evidenced in the Covenant of Grace. 

"I will not only tell thee what I am able to do, I will not only express to thee in general, that I will deal well with thee, that I have a willingness and ability to recompense thee, if thou walk before me, and serve me, and be perfect; but I am willing to enter into Covenant with thee, that is, I will bind myself, I will engage myself, I will enter into bond, as it were, I will not be at liberty any more, but I am willing even to make a Covenant, a compact and agreement with thee" 
(Miller, Seventeenth, pgs. 380).

The New England Puritan theological tradition was “an Augustinian strain of piety" (Miller, Seventeenth, pg. 8).  It called God the reason of all things, and the possibility of harmonic union of God and man it called Eden.  Disharmony was sin.  Awareness of the possibility of Eden was divine grace and the struggle to live in the light of that awareness was called faith.  Failure to live in that light destined the sinner for damnation (Miller, Seventeenth, pg. 8). The covenant reflected their piety. 

"The logic of the covenant had been clear, whether applied to individuals or to nations; one enters into the bond, he sins, and is afflicted, according to explicit terms; he confesses his sin, the affliction is removed, he is restored to the covenant" 
(Miller, Colony, pg. 197).

The only recourse to affliction was prayer and repentance, to be expressed through confession of the sins that brought the misfortune.  It was the duty of the civil authorities to pursue and punish those who refused to confess and repent 
(Miller, Colony, pg. 198).

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