Why would God leave the 99 to find 1?

The concept of leaving the 99 to find the one is from the Parable of the Lost Sheep, which is found in Matthew 18:10–14 and Luke 15:3–7. In this parable, the shepherd has 100 sheep, 99 of which are accounted for, and one which is missing. He leaves the 99 sheep to go find that one that is lost. But the point of the parable is the finding of the one, not the leaving of the 99. This is a parable about salvation.

Jesus told this parable in response to the Pharisees and scribes grumbling against Him for spending time with sinners (Luke 15:1–2). While the Pharisees did not associate with sinners, Jesus did—and His behavior was confusing to them. Jesus openly rebuked the Pharisees and scribes for their self-righteous hypocrisy (Matthew 23:28). What the Pharisees didn't understand was that Jesus was going after the one who was lost. He was extending saving grace to sinners.

In the parable, the 99 sheep are already safe with the shepherd. Jesus is not saying that He abandons His followers. Rather, the point of the parable is His pursuit of the lost and His joy when people come to Him for salvation. In Luke's gospel the Parable of the Lost Sheep is followed by the Parable of the Lost Coin and the Parable of the Lost Son (the Prodigal Son). These parables are about the salvation offered in Jesus Christ. The Parable of the Prodigal Son ends with the eldest son remaining outside the father's celebration when the younger son returns. The younger son had demanded his inheritance early and then squandered it only to find himself in desperate need. He realized his father could help him and came to understand his father's graciousness; he returned home with a repentant heart. The father saw the son a far way off, ran to him, covered his shame, and rejoiced at his return. But the older son, who had remained with the father, refuses to come to the celebration, even when his father goes to him. The elder son reveals his lack of love for the father. Though he seemed to be loyal he, too, had rejected his father's love and treated him with contempt. This is a rebuke against the religious leaders. Outwardly they appeared to be following God, but their hearts were far from Him. Jesus goes after the sinner and offers salvation, whether that sinner be one society labels as such or one wrapped up in his own self-righteousness. The point of Jesus' complementary parables is His eagerness to save and His great joy when someone comes to Him in faith and receives that salvation.

In the Parable of the Lost Sheep the shepherd leaves the 99 to go find the one that is missing. He goes after the one sheep who is vulnerable and alone, the one who is lost and in danger of being attacked by a wild animal. This is a metaphor of how Jesus came to seek and save all who are lost: "For the Son of Man has come to save that which was lost" (Matthew 18:11, NKJV; see also Luke 19:10). When we believe in Jesus Christ as Lord, He is our Savior and our Good Shepherd. Jesus said: "I am the good shepherd. The good shepherd lays down his life for the sheep" (John 10:11). Jesus laid down His life that we might be forgiven of our sin and rescued from eternal death (John 10:10; Romans 5:1–11; John 3:16–18). It is well worth it to Jesus to seek and save the lost sheep, knowing that the alternative for the lost is an eternity of separation from God. He wants to save all who are lost, for He is "not wishing that any should perish, but that all should reach repentance" (2 Peter 3:9).

When the lost sheep is found and brought home, there is great celebration: "And if he finds it, truly, I say to you, he rejoices over it more than over the ninety-nine that never went astray. So it is not the will of my Father who is in heaven that one of these little ones should perish" (Matthew 18:13–14). Again, the point is not that the shepherd leaves the 99, but his pursuit of the one and his joy at retrieving it.

Jesus not only brings us as sheep into the fold; He leads, guides, and protects us as we follow Him. He is our everlasting Shepherd. Perhaps the most memorable description of the Lord as our shepherd is found in Psalm 23:

The LORD is my shepherd; I shall not want.
     He makes me lie down in green pastures.
He leads me beside still waters.
     He restores my soul.
He leads me in paths of righteousness
     for his name's sake.
Even though I walk through the valley of the shadow of death,
     I will fear no evil,
for you are with me;
     your rod and your staff,
     they comfort me.
You prepare a table before me
     in the presence of my enemies;
you anoint my head with oil;
     my cup overflows.
Surely goodness and mercy shall follow me
     all the days of my life,
and I shall dwell in the house of the LORD

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