Mother Base/FOB: Can I climb onto a pipe from the top

Happen to me as well. I just re-did the mission and saved him again. Only this time i put him in the SickBay so he would heal. Youll notice the Injured bar goes down after a period of time and then he will be healthy and ready to go. Hope this helped

This cut-scene happens when morale drops to a very low point at Motherbase. Morale will decrease over time when you have not visited it in a while. Sometimes you will get certain events that trigger it additionally and you will see "Morale has decreased" on the screen in the notification area.

For those interested the cut-scene is here: Low Morale MGS5