Romans 5:14: "Yet death reigned from Adam to Moses, even over those whose sinning was not like the transgression of Adam, who was a type of the one who was to come."
Romans 5:17-19: "17 For if, because of one man's trespass, death reigned through that one man, much more will those who receive the abundance of grace and the free gift of righteousness reign in life through the one man Jesus Christ.
"18 Therefore, as one trespass led to condemnation for all men, so one act of righteousness leads to justification and life for all men. 19 For as by the one man's disobedience the many were made sinners, so by the one man's obedience the many will be made righteous."
John 10:14-16: "14 'I am the good shepherd. I know my own and my own know me, 15 just as the Father knows me and I know the Father; and I lay down my life for the sheep. 16 And I have other sheep that are not of this fold. I must bring them also, and they will listen to my voice. So there will be one flock, one shepherd.'"
John 8:31-32: "31 So Jesus said to the Jews who had believed in him, 'If you abide in my word, you are truly my disciples, 32 and you will know the truth, and the truth will set you free.'"
John 8:36: "'So if the Son sets you free, you will be free indeed.'"
Genesis 3:1-13: "1 Now the serpent was more crafty than any other beast of the field that the LORD God had made.
"He said to the woman, 'Did God actually say, "You shall not eat of any tree in the garden"?' 2 And the woman said to the serpent, 'We may eat of the fruit of the trees in the garden, 3 but God said, "You shall not eat of the fruit of the tree that is in the midst of the garden, neither shall you touch it, lest you die."' 4 But the serpent said to the woman, 'You will not surely die. 5 For God knows that when you eat of it your eyes will be opened, and you will be like God, knowing good and evil.' 6 So when the woman saw that the tree was good for food, and that it was a delight to the eyes, and that the tree was to be desired to make one wise, she took of its fruit and ate, and she also gave some to her husband who was with her, and he ate. 7 Then the eyes of both were opened, and they knew that they were naked. And they sewed fig leaves together and made themselves loincloths.
"8 And they heard the sound of the LORD God walking in the garden in the cool of the day, and the man and his wife hid themselves from the presence of the LORD God among the trees of the garden. 9 But the LORD God called to the man and said to him, 'Where are you?' 10 And he said, 'I heard the sound of you in the garden, and I was afraid, because I was naked, and I hid myself.' 11 He said, 'Who told you that you were naked? Have you eaten of the tree of which I commanded you not to eat?' 12 The man said, 'The woman whom you gave to be with me, she gave me fruit of the tree, and I ate.' 13 Then the LORD God said to the woman, 'What is this that you have done?' The woman said, 'The serpent deceived me, and I ate.'"
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The verses from Romans 5 appear most clearly at the beginning of the first verse, but they also inform the hymn as a whole. The text from Genesis (although mostly just verse 8) bridges the end of the first verse and the beginning of the second ("We all have fled that evening voice / That sought us as we ran."). The end of the second verse ("Each man his brother slew") references the story of Cain and Abel in the next chapter, Genesis 4.
The Good Shepherd from John 10:14-16 is referred to in the third and fourth verses.
The two passages from John 8 appear in the fifth verse, specifically in the line "Thou Son, O set us free."
