It was never exactly clear why Onesimus ran from his master, although the implications were that he had destroyed or stolen a part of his masterr's property. But what is clear is that whatever led him away was still on Godd's radar. Onesimus ended up under the care of Paul, perhaps the first century church's most powerful apostle. Paul took Onesimus in and cared for him like a son.
Paul took relationships very seriously, enough so that he made it a priority to emphasize proper relationships in several of his letters to the churches. Those he took under his care throughout his ministry not only embraced the Gospel but went on to become life-changing leaders within the various churches scattered throughout the region, including Aquila and Priscilla, Epaphras, Aristarchus and even Philemon. Others that he frequently traveled with no doubt were edified and strengthened in their faith through Paul's example, such as Silas, Barnabas, Timothy, Luke, Titus and Tychicus, among others.
So when it came to his letter to Philemon, Paul was doing nothing different than his normal ministry. Philemon was the leader of the church that met in his home in Colossae. As a leader, he was to set the example in speech and conduct. It was important to Paul that Philemon even set the example in the restoration of a fallen brother. Onesimus was not saved when he left Philemon's home, but he became a Christian under the close and personal care of Paul. As a Christian, it was Philemon's responsibility to choose to accept Onesimus' repentance and open his home to him once again. Only the relationship was not to be a master to slave, but brother to brother.
Philemon was not the only one who had a responsibility, however. Onesimus needed to return to his master and repair the broken relationship, despite the severity of the consequences he could face under Roman law. Perhaps Paul, in his Gospel message to Onesimus, stressed the importance of restoring broken relationships, both with God and man. He was not to leave anything undone. Running away from Philemon's home was not the answer to dealing with issues. Onesimus needed to return to Philemon and be accountable for his actions. Paul had no doubt commanded Onesimus to face whatever consequences in order to have closure to his old way of life. Now that Onesimus was a Christian, he had a clean slate spiritually. But he needed to make right that which he had wronged so that he could experience the peace of reconciliation.
Paul's letter to Philemon exemplified the whole of his ministry: be reconciled and live in unity with one another. Whether it was restoration with God or with fellow believers, the blessing of harmony is important to God, and therefore was equally important to Paul. As an apostolic leader, Paul had the authority to command Philemon to embrace Onesimus. But he chose not to use his God-given authority. Instead, he appealed to Philemon as a brother and a friend, knowing that only through love, exhortation and encouragement, true restoration could take place.