An absolutely emotional moment and the best in the whole game in my opinion.
It happened after 150+ hours of playthrough for me so it hit me badly. At first I thought "hey, some story is happening!", then "what's with Kojima's zombie fetish anyway", but then seeing all the soldiers who were in there made me think "wait what the fuck is going to happen? we're going to save them, right?"
Then I reached the top and shit hit the fan. I have to kill each and every one of them. Some are scared, one guy even fires at you when he realizes what's about to happen. And there's this "-60 Heroism" and "Staff member has died" that won't stop. Also, the rooms in the quarantine platform re-use Paz's room, giving the whole thing a very strange atmosphere that makes you wonder if it's even real at all, because of how strange and twisted it is (you have to kill several guys you saw hang around Mother Base, who don't react like usual enemies do, and because they trusted you, it feels like The Boss over and over again).
Then there is the room with the soldiers humming the PW theme and letting Venom do the right thing, and that what made me feel the worst. Then there is the one guy who might not have it - lol nevermind. You go inside thinking you might salvage something out of this, but in the end you have to kill each and every one of your soldiers who were in there, at close range (and trying to headshot to make it quick but missing and hurting them more), some of them being S ranks and some of them being recognizable from earlier. Giving you the goggles was a dick move too, since in the end you realize no one is safe, not even that one guy.
Then you have the following cutscene, with the nightmare-ish transition from Venom to Demon Snake and the audio flashback to the very first scene in the game (Outer Heaven). Then you have one of the most anticipated cutscenes from the trailers. I think this part of the story really cements Venom as his own character, by giving him his own "The Boss" moment.
Overall the on-rail sections of the game were fantastic and it's sad there weren't more of them.