Setting the scene
One year before his death, prior to Passover in 29 A.D., Jesus is at his peak of popularity. He decides to travel to Gennesaret (near Capernaum) after his ghost like appearance to his disciples on the Sea of Galilee.
The people living in Gennesaret recognize Jesus the moment he makes land (Mark 6:53). They fervently rush to gather all the sick and diseased they can find so that they can be healed.
Then they RAN through all the country around, and began to carry those who were sick on stretchers, taking them wherever they heard that He was. And wherever He entered into villages or cities or fields, they laid in the marketplaces those who were sick . . . (Mark 6:55 - 56, HBFV throughout).
The crowds around Jesus continue to grow as those who were either part of or heard of his recent miraculous feeding of 5,000, near Bethsaida, track him down in Capernaum (see Mark 6:30 - 42, John 6:22 - 24, 59).
Jesus, entering a Capernaum synagogue on the Sabbath (John 6:59), taught the following to the Jews and disciples gathered.
"I am the living bread, which came down from heaven; if anyone eats of this bread, he shall live forever; and the bread that I will give is even My flesh, which I will give for the life of the world . . .
"Truly, truly I say to you, unless you eat the flesh of the Son of man, and drink His blood, you do not have life in yourselves" (John 6:51, 53).
Those assembled to worship God were shocked and offended at what they heard (John 6:60). They were well aware that God commanded ancient Israel to not eat blood even if it was in a clean animal killed for food (Leviticus 7:26 - 27, 17:10 - 15). They also knew that the Eternal promised to punish, severely, those who knowingly broke this prohibition.
Word of what Jesus said in the synagogue quickly spreads to others who had followed him into Capernaum. They too found his statements absurd, unbelievable and offensive. Their lack of understanding led them to leave, to no longer associate with him or acknowledge he was the Messiah.
From that time, many of His disciples went back and walked no more with Him (John 6:66).
The Bible does not record exactly how many disciples left Jesus. The scale of the apostasy, however, was significant enough to shake the faith of the twelve apostles. The Lord quickly moved to shore up their belief that he was the Messiah.
Therefore, Jesus said to the twelve, "Are you also desiring to go away?" (John 6:67).
Peter, whose impulsivity usually led to him speaking first, answered for the disciples by reaffirming they still believed he was, "the Christ, the Son of the living God" (John 6:69).
Reason for separation
The Lord chose, in part, to make his statements when he did because he knew it would winnow out those not called by the Father. He knew that those who did not have their minds open to the truth would ultimately reject his message (John 6:36 - 37, 44 - 45, 64 - 65).
Those who heard Jesus' statements completely misunderstood his words. They interpreted them in a literal fashion, believing he was crazy for condoning what amounted to cannibalism!
Jesus' statements were symbolic of the bread and wine he would introduce to His twelve disciples at His final Passover (Matthew 26:26 - 28).
It should be noted that the Lord was not condoning some kind of weekly communion among church members. He was, however, advocating the absolute necessity (see John 6:51, 53 - 56) of commemorate his death, on a yearly basis, through the Christian Passover (1Corinthians 10:16 - 17, 11:23 - 28). This feast day would be kept by the early New Testament church and is still kept by true believers.
What was true in the first century with the disciples is also true today. Those who are only superficially attracted to Jesus and his message eventually leave. Those who stay, however, and obey his words can look forward to receiving the gift of eternal life as, "The one who eats My flesh and drinks My blood has eternal life, and I will raise him up in the last day" (John 6:54).