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The peculiar character of the epistle as the expressions of Paul's heart in sight of the Church's failure and departure
The second epistle to Timothy has a very peculiar character. It is the expression of his heart, who outside Palestine had, under God, founded and built the assembly of God on earth, and it was written in sight of its failure, and its departure from the principles on which he had established it. God remained faithful; His foundation was sure and immovable; but the work committed into the hands of men was already enfeebled and decaying. The consciousness of this state of things, which moreover betrayed itself in the way in which the apostle himself was then forsaken, oppressed his heart; and he pours it out into the bosom of his faithful Timothy. By this means the Spirit instructs us in the solemn truth, that the church has not kept its first estate, and sets before us the ways of safety for those who seek God, and desire to please Him, in such a state of things as this.
The apostle John's witness
The apostle John gives the history of the fall of the assembly here below, and of its judgment, and that of the world likewise. He also sets before us a life which, apart from all questions of the assembly's condition, abides ever the same, which renders us capable of enjoying God, and makes us resemble Him in His nature and character.
Paul's painful experience that of all the servants of God; man's failure; the sure foundation
As a witness John was to remain until the Lord came: but Paul sees for himself the ruin of that which he had built and watched over so faithfully. He had spent himself for the assembly, accomplishing that which was behind of the sufferings of Christ; and he had to see that which he had so much loved (which he had cared for even as a mother cherishes her nursling which he had planted as God's plant on the earth) grow feeble as to its condition and testimony in the world, depart from the source of strength, and become corrupt. What a painful experience! But it is that of the servant of God in all ages and in all dispensations. He sees indeed the power of God acting to plant the testimony on earth, but he sees that men soon fail in it. The house inhabited by the Holy Ghost becomes dilapidated and in disorder. Nevertheless (and we love to repeat it with the apostle) the sure foundation of the Lord abides for ever. Whatever may be the condition of the whole company, the individual is always to depart from all iniquity, and to maintain, by himself if need be, the true testimony of the name of the Lord. This can never fail the faithful soul.
The apostle's comfort when afflicted and forsaken
In view of the mixture and confusion which began to show itself in the assembly, the apostle's comfort was founded on these two principles, while remembering and joyfully availing himself of the communion and faithfulness of some precious souls. He had such as Timothy and Onesiphorus, amid the afflictions of the gospel and the sorrow of being forsaken by so many who were seals to his testimony before the Lord.Synopsis by John Darby