John 16 Commentary

What did Jesus mean by "put you out of the synagogues" (John 16:2)?
They will be rejected religiously, socially and economically (details) not just in one town but everywhere (notice the plural) they go to preach the Gospel.

What else does Jesus say will happen to them in John 16:2?
They will lose not just their social and economic lives, but eventually their physical lives as well.

Is that what really happened to them?
According to Acts 12, James was stabbed to death. According to oral historical commentary, Andrew and Peter were crucified, the latter presumably upside down, Bartholomew was flayed alive, Matthew was burned alive, Thomas was speared to death, James the son of Alphaeus was stoned to death, Thaddaeus was clubbed to death, and Simon the Zealot was sawn in half (see Judas).

Is it true that their killers thought that they were offering "God service" (John 16:2)?
The mindsets of their respective killers are not recorded, but history is full of people who killed thinking that they were serving God. During the Dark Ages, the Crusaders killed untold numbers of Jews and Arabs in the name of God. During the Middle Ages, the Catholics killed untold numbers of Protestants and Jews in the name of God. And more recently, the self-declared Protestants of Nazi Germany killed millions of Jews while wearing uniforms whose belt buckle bore the inscription, "Gott Mit Uns," which means in German, "God With Us."

Why?
For one, Satan kills three birds with one stone: instigate mayhem, dishonor God's name, and make people want to have nothing to do with God, who they think caused the mayhem. For another, the people who were instigated by Satan "have not known the Father nor Me" (John 16:3 below), who is the Word of God. Had they read the Bible for themselves instead of blindly trusting their national and/or religious leaders who supposedly had read the Bible, they would have known that such killings go against everything Jesus said and did.

In what sense will the killers have "not known" (John 16:3) God the Father or Jesus?
They certainly will lack a relationship with the Father or Jesus, and they could also lack knowledge of the truth about the Father and Jesus.

Will any of this catch Jesus off-guard?
"But these things I have told you, that when the time comes, you may remember that I told you of them" (John 16:4). God knows everything, and He wanted His disciples to know that He knew in advance.

Why would "sorrow" have "filled" (John 16:6) the disciples' hearts?
Jesus had told them that one of them will betray Him, that Peter will deny Him, and that He will leave them, all of which already troubled them. Now, He was saying that they will be rejected everywhere they go, and end up getting killed.

Who is the "Helper" (John 16:7) Jesus will send after His departure?
The Holy "Spirit of truth" (John 16:13).

By "Helper," is Jesus calling the Holy Spirit His assistant or someone who will help the disciples?
παρακλητος (Parakletos), the original Greek word translated "Helper" in John 16:7, means someone who gives comfort or counsel, so Jesus is referring to the Holy Spirit's role to the disciples, not His position vis-a-vis Jesus. Jesus referring to the Holy Spirit as the "Helper" is all the more appropriate now since "sorrow has filled" the disciples' "heart" and they need to be comforted, and that need will increase in the coming hours.

How is it to the disciples' "advantage" (John 16:7) that Jesus goes away and the Holy Spirit comes?
"Do you not know that your body is the temple of the Holy Spirit who is in you, whom you have from God...?" (1 Corinthians 3:16). Having God dwell inside of us is even better than having Him next to us.

Has the Holy Spirit taken up residence inside you?