A similar question, focusing on Japanese aircraft left in the air following the Battle of Midway, was answered by /u/kieslowskifan here. To sum it up, most of the aircraft left airborne after the bombings of Akagi, Kaga and Soryu landed on the undamaged Hiryu. After Hiryu was bombed, the remaining airborne CAP pilots mostly ditched near the escorting destroyers and cruisers. A few others bailed out, and were also rescued by destroyers and cruisers. If the aircraft were operating near friendly territory, then they would tend to try to make that first, but ditching was common.