Milton, who lived at the same time as Biddle and shared many of his views, was not as outspoken as Biddle, preferring to lead his life outside prison.  In volume two of his "Treatise of True Religion" he says, "The Arians and Socians are charged to dispute against Trinity.  They affirm to believe the Father, Son and Holy Ghost according to Scripture and the Apostolic Creed.  As for terms of trinity, tri-unity, co-essentiality, tri-personality, they reject them as scholastic notions not to be found in scripture which by general Protestant maxim is plain and perspicuous abundantly to express its own meaning in the properest words belonging to so high a matter and so necessary to be known, a mystery indeed in their sophistic subtleties but in scripture a plain doctrine."³⁸

Power exercised by Popes, Councils, Bishops and press byters

In another book he was more direct.  He said that the power exercised by Popes, Councils, Bishops and Presbyters was to be classified as among the rankest and most odious of tyrannies.  He continued, "All imposition of ordinances, ceremonies and doctrines are an unwarranted invasion of Liberty."³⁹

The poet did not openly defy the civil authority of the country, but he kept to himself as a protest against the bigotry and intolerance of the established church.  Like a number of leading intellectuals, he stopped going to any church.  Dr. Johnson said of Milton, "He has not associated with any denomination of Protestants.  We know rather what he was not than what he was.  He was not of the Church of Rome.  He was not of the Church of England. Milton grew old without any visible worship. In his distribution of his hours there was no hour of prayer - his work and his meditation were an habitual prayer."⁴⁰

It is clear that Dr. Johnson was not aware of a book written by Milton and discovered nearly a hundred and fifty years after his death in 1823.  The manuscript was found in the old State Paper Office in Whitehall and was entitled "A Treatise Relating to God."  Written while he was a Latin secretary to Cromwell, it was obviously not intended to be published during Milton's life.

In Book I, chapter two, Milton writes about the attributes of God and in particular the Divine Unity:

Though there be not a few who deny the existence of God, for the fool hath said in his heart there is no God'. Psalm 14.1, yet the Detty has imprinted upon the human mind so many unquestionable tokens of Himself and so many traces of Him are apparent throughout the whole of nature that no one in his senses can remain ignorant of truth.  There can be no doubt that everything in the world by the beauty of its order and the evidence of a determinate and beneficial purpose which prevades it, testifies that some supreme efficient Power must have pre-existed by which the whole was ordained for a specific end.

No one however can have right thoughts of God with nature, or reason alone as his guide, independent of the word or message of God...God therefore has made as full a revelation of Himself as our minds can conceive or the weakness of our nature can bear...Such knowledge of the Deity as was necessary for the salvation of man.  He has Himself of His goodness been pleased to reveal abundantly...The names and attributes of God either show His nature or His divine power and excellence.

Milton then lists some of the attributes of God: Truth, Spirit (I am that I am), Immensity and Infinity, Eternity, Immutability (I change not), Incorruptibility, Immortality, Omni-presence, Omnipotence, and finally, Unity, which he says "proceeds necessarily from all the forego/o:p>

Jehova. He is God, there is none besides Him.

(Deuteronomy 4.35)

Jehova, He is God in the heavens above and upon the earth beneath: there is none else.

(Deuteronomy 5.39)

I, even I, am He and there is no God with Me.

(Deuteronomy 32.39)

...that all the people of the earth may know that Jehova is God and that there is none else.

(I Kings 8.60)

...Thou art the God, even Thou alone, of all the kingdoms of the earth. (2 Kings 19.15)

Is there a God besides Me? Yea, there is no God.

(Isaiah 44.8)

I am Jehova and there is no God besides Me.

(Isaiah 45.5)

There is no God else besides Me..there is none besides Me.(Isaiah 45.21)

I am God and there is none else. (Isaiah 45.22)

Commenting on the above verse, Milton says, "that is, no spirit, no person, no being beside Him is God for "none" is a universal negative."

I am God and there is none else.  I am God and there is none like Me. (Isaiah 46.9)

...what can be plainer, what more distinct, what more suitable to general comprehension and the ordinary forms of speech, for the purpose of impressing on the people of God that there was numerically One God and One Spirit in the common acceptation of numerical unity?  It was in truth fitting and highly agreeable to reason that the first and consequentially the greatest commandment to which even the lowest of the people were required to pay scrupulous obedience should be delivered in so plain a manner that no ambiguous or obscure expressions might lead his worshippers into error or keep them in suspense or doubt.  Accordingly, the Israelites under the law and their prophets always understood it to mean that God was numerically one God besides whom there was none other, much less any equal. For the schoolmen had not as yet appeared who through their confidence in their own sagacity, or more properly speaking on arguments purely contradictory, impunged the doctrine itself of the Unity of God, which they pretended to assert. But as with regard to the omnipotence of the Deity, it is universally allowed, as has been stated before, that he can do nothing which involves a contradiction: so it must always be remembered in this place that nothing can be said of the One God which is inconsistent with his Unity, and which assigns to him at the same time the attributes of unity and plurality.  Mark 13.29-32: "Hear O Israel, the Lord our God is one Lord." To which answer the scribe asserted, "Well, Master, thou hast said the truth: for there is One God, and there is none other than He."Milton then goes on to discuss the nature of the Holy Spirit.  The Scripture he says is silent, on its nature, in what manner it exists, and from whence it arose.  He continues, It is exceedingly unreasonable not to say dangerous that in a matter of so much difficulty believers should be required to receive a doctrine represented by its advocates as of primary importance and of undoubted certainty of anything less than the clearest testimony of Scriptures, and that a point that is confessedly contrary to reason should nevertheless be considered as susceptible of proof from human reason only or rather from doubtful and obscure disputations.

Milton then draws the following conclusions from his knowledge of the Bible:  The Holy Spirit is not omniscient.  It cannot be said that because the Holy Spirit carries out the work of God, therefore it is part of God.  If this was so then why is the Holy Spirit called the Comforter, who will come after Jesus, who speaks not of himself nor in his own name, and whose power therefore is acquired.  (John 16.7-14)  It therefore becomes clear that instead of accepting the term "Comforter" in its obvious sense as a prophet who will come after Jesus, to call him Holy Spirit and yet call him God creates a confusion which cannot be ended.⁴¹

Milton agrees with Arius that Jesus was not eternal. He says it was in God's power to create or not to create Jesus.  He concludes that Jesus was born "within the limits of time." He is at a loss to find any passage of scripture which would support the "eternal generation of Jesus."  The hypothesis that Jesus, though personally and numerically another, is yet essentially one with God is strange and repugnant to reason.  This dogma does violence not only to reason but also to scriptural evidence.  Milton agrees with the "Israelitish people" that God is One and only God.  It is so evident that it requires no explanation, that God alone is the self-existing God; and that a being that is not self-existing cannot be God.  He concludes,It is wonderful with what futile subtleties or rather with what juggling artifices certain individuals have endeavored to elude or obscure the plain meaning of the passages of the Scriptures.⁴²  

  Milton says that the Holy Ghost was inferior to both God and Jesus, since his duties were to carry messages from one to the other.  On his own he could do nothing.  He is sub-servient and obedient to God in all things.  He is sent by God and is given nothing to speak of himself.

Milton felt he could not express these views openly, for to have done so would have been to endanger his own personal safety, and to expose himself to the same treatment that Biddle and many others had suffered.  In 1611, that is within Milton's lifetime, two men called Mr. Legatt and Mr. Wightman, were burnt alive with the king's permission because they believed that there was no Trinity of persons, Father, Son and Holy Spirit, in the Unity of Goodhead; that Jesus Christ was neither the natural true son of God, nor of the same substance, eternity and majesty with the Father in respect to his godhead; and that Jesus Christ was a man only and a mere creature, and not God and man together in one person.  Milton's silence while he was alive was therefore an understandable one.