The disciples are confused by Jesus' cryptic message about his departure and return. Jesus is speaking of his upcoming death, resurrection, and ascension. When he says, "In a little while you will see me no more," he is referring to his impending crucifixion, where he will be taken from them. "Then after a little while you will see me" points to his resurrection, when he will appear to them again, bringing joy and affirmation of his victory over death.
The phrase "because I am going to the Father" indicates Jesus' ascension, where he returns to his divine glory and completes his earthly mission. This transition marks the beginning of a new era where the Holy Spirit will be sent to guide and comfort the disciples in Jesus' physical absence. This passage encourages believers to trust in the divine plan, even when it is not fully understood, and to hold onto the hope and assurance of Jesus' continual presence through the Spirit. It reassures Christians that periods of confusion or sorrow are often followed by clarity and joy in God's timing.