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.
God is a Father. He counts His kids. He rejoices that some are safely in Christ, prepared for eternity and nestled near His heart. But some are missing. The Father sent Jesus on a rescue mission “to seek and to save the lost” (Luke 19:10). God does not abandon the 99. They are already safely in His kingdom, attended by His angels, and guided by His Holy Spirit (Romans 8:14; Hebrews 13:5).
We were all lost at one time, and the Lord came after us. If He had not taken the initiative, no one could be saved (John 6:44). So, when our Good Shepherd wants to pursue another lost lamb, the 99 who are in the fold can joyfully support the rescue.
The 99 are still important to Him, but He knows the flock is not complete without the lost sheep. And a good shepherd always goes after the lost sheep.
“I tell you that in the same way there will be more rejoicing in heaven over one sinner who repents than over ninety-nine righteous persons who do not need to repent.” – Luke 15:7
Jesus leaving the 99 to find 1 seems crazy until you are that 1.