Some of the Scriptures cited in our church confession indicate that we must be “set apart as a local church from all affiliations, fellowship, and cooperation with those who deny the cardinal doctrines of the true Christian faith.”
First, 2 Corinthians 6:14–17 states this: 14 Do not be unequally yoked with unbelievers. For what partnership has righteousness with lawlessness? Or what fellowship has light with darkness? 15 What accord has Christ with Belial? Or what portion does a believer share with an unbeliever? 16 What agreement has the temple of God with idols? For we are the temple of the living God; as God said, “I will make my dwelling among them and walk among them, and I will be their God, and they shall be my people. 17 Therefore go out from their midst, and be separate from them, says the Lord, and touch no unclean thing; then I will welcome you.
This text and especially the first verse has been regularly cited by gospel-believing Christians as to why a local church cannot extend Christian fellowship to another so-called church if it denies a fundamental doctrine of the Christian faith (e.g., the deity of Christ, His substitutionary death, the reality of miracles, inerrancy, salvation through Christ alone, the second coming). A group of believers who are together the temple of the living God cannot yoke, partner, share, or agree with unbelievers, lawlessness, darkness, Belial, and idols. Thus, if among them, we “go out from their midst, and be separate from them.
Second, 2 John 9–11 states this: 9 Everyone who goes on ahead and does not abide in the teaching of Christ, does not have God. Whoever abides in the teaching has both the Father and the Son. 10 If anyone comes to you and does not bring this teaching, do not receive him into your house or give him any greeting, 11 for whoever greets him takes part in his wicked works.
“The teaching of Christ” mentioned here is that Jesus Christ has come in the flesh (cf. 2 John 7). If Jesus is not man, then we have lost a human substitute who died for us on the cross. We have lost the gospel altogether. And so, as Christians, John commands us not receive him into our house or wish him well on his way. We would otherwise take part in his wicked words and lose our full reward (2 John 8).
Third, 2 Timothy 3:1–9 describes false teachers and gives this command in 2 Timothy 3:5: “Avoid such people.” We don’t call them Christians, and we cannot partner with churches or organizations that intentionally elect and keep false teachers as their leaders.