What is the mystery of iniquity?
The mystery of iniquity is the hidden, ongoing work of Satan's spirit of rebellion in humanity, already active in the world and destined to be fully revealed in the Antichrist before Christ's return.
The mystery of iniquity begins with the meaning of iniquity itself: a deep rooted rebellion against God's law that goes beyond single sinful acts. It is corruption and moral evil rooted in a desire to pursue one's own agenda against God's will. Scripture traces this spirit back to Satan, who was perfect in his ways until iniquity was found in him (Ezekiel 28:15). It was a single unlawful thought, hidden in his imagination, that corrupted him and separated him from God. That same spirit of iniquity is what Satan has since spread to mankind, entering even at conception, as David wrote, "Behold, I was shapen in iniquity; and in sin did my mother conceive me" (Psalm 51:5). From birth this spirit works within the flesh, using the law of sin and death to bring forth its desires, so that every person is by nature a child of wrath, walking according to the prince of the power of the air (Ephesians 2:1-3).
Paul calls this present, hidden operation "the mystery of iniquity" because it works secretly, disguising itself so that people believe the sinful cravings Satan produces in them are simply their own desires. "For the mystery of iniquity doth already work: only he who now letteth will let, until he be taken out of the way" (2 Thessalonians 2:7). The Holy Spirit is the one who restrains its full effect. This mystery manifests in two ways: first, through the coming Antichrist, a man who will embody the devil the way Jesus embodies God, appearing as a mere man while actually being Satan's manifestation; and second, through unbelievers, in whom the spirit of iniquity already works because they lack the Holy Spirit. Those who perish are deceived by "all deceivableness of unrighteousness," which keeps them from repentance because they did not receive the love of the truth (2 Thessalonians 2:8-10).
This deception is what keeps Satan's presence a mystery. He works evil while hiding his involvement, so that people take his workings as their own, saying things like "I can never change" or "I have always been like this," when in truth it is the spirit of iniquity working in them. Because righteousness has no fellowship with unrighteousness, iniquity separates a person from God the moment it is regarded in the heart, as Isaiah declared: "your iniquities have separated between you and your God" (Isaiah 59:2), and as the Psalmist affirmed, "If I regard iniquity in my heart, the Lord will not hear me" (Psalm 66:18).
God eventually addressed this hidden mystery by giving the Law of Righteousness to Israel through the Ten Commandments. This exposed the presence of the enemy within, since hearing God's righteousness pricked the conscience yet the devil would not allow obedience, creating the war described in Romans 7 between the law of the mind and the law of sin in the members. This conflict revealed what had been concealed and led the convicted soul to cry out, "O wretched man that I am! who shall deliver me from the body of this death?" (Romans 7:24), pointing to the need for deliverance through Jesus Christ.
The scriptures
For the mystery of iniquity doth already work: only he who now letteth will let, until he be taken out of the way. And then shall that Wicked be revealed, whom the Lord shall consume with the spirit of his mouth, and shall destroy with the brightness of his coming: Even him, whose coming is after the working of Satan with all power and signs and lying wonders, And with all deceivableness of unrighteousness in them that perish; because they received not the love of the truth, that they might be saved.
Behold, I was shapen in iniquity; and in sin did my mother conceive me.
And you hath he quickened, who were dead in trespasses and sins; Wherein in time past ye walked according to the course of this world, according to the prince of the power of the air, the spirit that now worketh in the children of disobedience: Among whom also we all had our conversation in times past in the lusts of our flesh, fulfilling the desires of the flesh and of the mind; and were by nature the children of wrath, even as others.
Thou wast perfect in thy ways from the day that thou wast created, till iniquity was found in thee.
Behold, the LORD’s hand is not shortened, that it cannot save; neither his ear heavy, that it cannot hear: But your iniquities have separated between you and your God, and your sins have hid his face from you, that he will not hear.
If I regard iniquity in my heart, the Lord will not hear me:
For I delight in the law of God after the inward man: But I see another law in my members, warring against the law of my mind, and bringing me into captivity to the law of sin which is in my members. O wretched man that I am! who shall deliver me from the body of this death?
For when we were in the flesh, the motions of sins, which were by the law, did work in our members to bring forth fruit unto death.
From the books
This answer is drawn from these passages in the Mary Banks Faith Library.