To “retain” something (v. 13) means to keep possession of it (Job 2:9). Before returning Philemon’s runaway slave, Paul thought about retaining him (v. 13) to “minster” unto him in prison. In those days, prisoners were literally fed bread and water (I Ki. 22:27), but in some cases they were allowed friends or servants to “minister” to them (cf. Mt. 25:43,44).
The Book of Philemon doesn’t teach Pauline doctrine, it illustrates them. When Paul says he thought of keeping Onesimus in Philemon’s stead, that illustrates how we are here “in Christ’s stead” (II Cor. 5:20). That means we should be beseeching sinners to be reconciled to God as He would.
Slaves were a man’s possession, however (cf. Lev. 25:45,46), so Paul wouldn’t keep him without Philemon’s permission (Phile. 1:14). He told him he would “benefit” for it at the Judgment Seat of Christ if he let him use his possession, as people today will benefit for letting missionaries use their cars, etc. But he explained he’d benefit more if he gave Paul use of his possession “willingly” and not “of necessity.” This illustrates how God will someday reward all of the money we possess that we give to the Lord, but we’ll benefit more at the Judgment Seat of we give in a “willing” way (II Cor. 8:12) and not “of necessity” (II Cor. 9:7).
If Philemon had retained Onesimus, he could only have had him as a slave until he died. But now that Paul was retaining him after leading him to the Lord, Philemon could have him back as a brother for all eternity (Phile. 1:15,16).
When Paul says Onesimus departed “for a season” (v. 15), that should remind you of the Jew who was blinded for a season when he tried to keep Paul from giving a Gentile the gospel (Acts 13:11).
So when Onesimus departed for a season so Philemon could receive him forever as a brother, that illustrates how Israel departed from God for a season so God could receive her forever in the kingdom. They “departed” in Acts 28:28,29 and their “receiving” will come in their kingdom (Ro. 11:15).
Paul can’t be saying Onesimus ran away so he could return to Philemon for ever. And he can’t be saying Philemon let him run away so he could return forever. No, it was God who wanted him to leave so he could get saved (I Tim. 2:4). But we have to be careful, for God says servants should obey their masters, not run from them (Eph. 6:5), so running away is a sin, and God never makes anyone sin.
But God knows how to use men’s sins to accomplish His will. God didn’t make Joseph’s brethren sin by selling him into slavery, but when He saw they hated him (Gen. 37:4) He gave him a dream saying he’d rule them, making them hate him enough to sell him (Gen. 37:8). That’s how Joseph could say God sent him into slavery (Gen. 45:7,8), using His Word in a dream. They just reacted sinfully to His Word.
And God used His word to get Onesimus to run away, His word through Philemon. He was a faithful Christian (Phile. 1:4-6), so was no doubt witnessing to Onesimus. He just resented hearing it from his high and mighty master, so reacted sinfully to it. But when he heard the gospel from Paul, someone beneath him in prison, he believed it.
So why does Paul say “perhaps” that’s what happened? Because there was an element of chance involved. God could make Onesimus want to run by giving him His word, but he couldn’t make him run 1200 miles to Rome and bump into Paul. The “hap” part of perhaps means something hap-pened to happen (Ruth 2:3) by chance (II Sam. 1:6). There’s such a thing as chance—luck (Ecc. 9:11). Moses believed in it (Deut. 22:6), as did the Lord (Lu. 10:31). God is not orchestrating our every move, He gave us free will.
So Paul is telling Philemon not to look at it as his slave running away, but to look at it all as God using sin and His Word and chance to “work together” for good (Ro. 8:28).
God also works through His people though. If Philemon didn’t forgive Onesimus, then all those things wouldn’t work together for good. It all comes down to you. If you’re not happy with your life, begin to obey God’s Word through Paul.