The Two Mysteries are The Mystery of Godliness and The Mystery of Iniquity.
The word mystery does have a pagan origin. It started in Babylon in the great rebellion against God and His commands. But God has taken the language of man and purified it for His own use.
Running down through the ages are two mysteries. They seem to be parallel, but someday they will meet. That will be a terrible time when absolute holiness comes face to face with the epitome of unrighteousness. It is hard to imagine the result.
The two mysteries are the mystery of godliness and the mystery of iniquity. The first one is of God; the latter is of the wicked one. The one is manifested in Christ Jesus. The other will be manifested in the Antichrist. Closer examination will reveal the terrible truth that one is a very close counterfeit of the other, so close that many will be deceived and led to destruction. So many people think Antichrist will be a wicked ruler out to make men sin, but in reality, he will be a counterfeit for The True Messiah. He will speak of love, peace, and kindness with generosity and demand people everywhere live a sinless life. But hiding behind those words is a false messiah. He will be accepted by "good" men everywhere, mainly in Israel, where they will let him become the high priest. Now, would Israel let one who is not a descendant of Abraham ever become the high priest and enter The Holy of holies in The Temple? So the false one must be able to prove he is of the Abrahamic line by DNA. So many think the Antichrist and the Beast are the same, but not according to Scripture. The Beast controls the military power of the air, the Antichrist the hearts and minds of the people, for we see from the Book of Revelation that many are deceived.
The mystery of godliness is expressed in Phil. 2:5-9, 'Christ Jesus, who being in the form of God thought it not robbery to be equal with God, but made Himself of no reputation, and took upon Him the form of a servant ...Wherefore God also hath highly exalted Him, and given Him a name which is above every name.'
The mystery of iniquity is expressed in Isaiah 14:13-14, 'I will ascend into heaven, I will exalt my throne above the stars of God, I will sit also upon the mount of the congregation ...I will ascend above the heights of the clouds, I will be like the Most High.' These are the words of Satan as he aspired to be equal with God. But Christ has that Holy place forever.
We are told about the mystery of godliness in 1 Timothy 3:15-16, '. . . the pillar and ground of the truth, and without controversy great is the mystery of godliness: God was manifest in the flesh, justified in the spirit, seen of angels, preached unto the Gentiles, believed on in the world, received up into glory.' The Lord came that He might declare or manifest the Father.
The pinnacle of the mystery of godliness is the administration (Dispensation) of The Mystery. It was a perfect secret, for we are told that it was hidden in God and also hidden from ages and generations. Other mysteries were not so completely hidden or secret as this perfect one.
This mystery is the program or purpose of the ages that man had never dreamed of before; he never saw anything about, never heard anything about it, and never even thought anything about it. The prophets of old searched for a period between Christ's ascending back to Heaven from whence He came and His Mighty return in the clouds, coming with countless groups of ten thousand angels each. They searched in vain for what God had hidden and what angels longed to see of the untrackable riches of Christ. God made the riches sure to us by hiding this Secret so that Christ Jesus our Lord could accomplish His Purpose. This secret concerns the headship of Christ over all things in all creation. It tells of a people chosen to have a place in heavenly places in the resurrection. It tells of all blessings which are spiritual and enjoyed in the Heavenly Places in Christ. And this Church of The Mystery is now making known (witnessing) to the principalities and powers in the heavenlies this Perfect manifold (variegated: multi-colored) Wisdom of God. The surprising thing about all this is the fact that these chosen people are all Gentiles (even though some are by birth Jews), not Israel.
After Acts 28:28, it was the avowed purpose of Paul to make all men see what is the fellowship of the mystery. That also should be our goal today; if so, be that we have trusted in this great gospel.
We understand that God's plan concerning Israel is still in abeyance. But we must not be careless. The mystery of iniquity is working in the world yet today. But there is a provision. We are to put on the whole armor of God and stand. We should be able to withstand the evil day.