"When therefore the Lord knew how the Pharisees had heard
that Jesus made and baptized more disciples than John,
(Though Jesus Himself baptized not, but His disciples,)
He left Judaea, and departed again into Galilee."
The end of chapter 3 is the last time that we hear from John in this particular Gospel. He is referred to again in later chapters, but his active speaking is over. The truth of the matter is that John truly did decrease while Jesus increased. Matthew 4 says that John was imprisoned about this time.
"When therefore the Lord knew how the Pharisees had heard that Jesus made and baptized more disciples than John...." The Lord was always about the work of leading people into the true kingdom of heaven. The souls of men are very important to God and should be to His Church as well. At about this point in Jesus' ministry, hostilities from Herod begin to arise (Matt. 4:12), and the unbelieving Jewish leaders start to cause contention toward the ministry of Jesus. The Lord exercises discretion and chooses to relocate for the purpose of continuing His Father's will. Christ's hour had not yet come. It was not time for Him to be handed over to the Jews and it was not God's will that He be executed by Herod; therefore, "He left Judea...." This word can be understood as to let go, or forsake. Discretion guided Him and kept Him in God's will by knowing when to leave and when to stay.