(This post contains some story spoilers, -ish.)
I have been having a lot of fun with this story chain of missions, but I broke it and thought I should mention it. (I ran this mission twice and it gets stuck at the same point.) So I am at the door I am supposed to finish opening after defeating the corrupted Alpha Team, and I took down the 2 that showed up but it will not let me progress and there are no others inside the entire mission, so I am sadly going to have to auto-complete the mission. (I was really hoping to see the ending too!)
A little background (yes I AM really good at breaking things):
When given the option I had 1 of the original team members removed and sent to the hospital.
Ran the mission where I lost 2 of my original 4 teammates. (When splitting up, I chose to go alone.)
3 replacements were put on the team, after that mission I requested all the replacements be removed and was told only 1 of them would be.
Ran final mission, choosing to go by myself, and only the 2 original members that were left on the team spawned for me to fight.
At any rate, I hope this might help someone, anyone, but doubt most make the bizarre story choices I do hehe. Props. ^.^