I just went through this. I recommend doing a couple of more story missions right away.

Yes focus on finishing the next few story missions because the thing will make you start losing stuff you don't wanna lose.

You need to handle it asap. If I remember correctly, basically every character including Ocelot and Miller are telling you to take care of it immediately, and you should listen. Bad shit will happen if you don't keep running story missions. It's not that long until you handle it.

1. Ignore anything other than story missions until the whole thing is resolved.

2. Before you start another story mission, see if you can figure out how to use the makeshift solution the game gives you. If you figure it out, you'll lose far less things as you do the story missions.

I lost a whole bunch of dudes because I did some side ops first but I needed the money and resources.

The game doesn't necessarily give you the best clues, but there is a way you can actually minimize the losses. If you can't sort that out though, just focus on main missions until the issue resolves itself.

Get this resolved ASAP. If you leave it sit it'll just keep eating away at you.

If you figure it out and act quickly Millar will inform you that you've done the right thing.

Like people have said power through the next few story missions. You can get minimal losses and I did actually figure out the problem and acted on it even though, I thought I was a crazy person, up until I finished those story missions and then it made sense. Well MGS sense atleast.

Definitely something you have to act on quickly, in both the story missions and figuring out the problem itself. The issue is if you don't look into the problem right away, you lose the ability to figure out exactly what everything has in common, thus forcing you to just crank out the missions before it goes too far. I actually really disliked this part, because I didn't look into the very minute it happened, so I lost the trail.

Here's a hint for anyone dealing with this: go read Brad's tweet linking to the bombcast that he posted on September 8th.

If your talking about what i think your talking about, hurry the fuck up and do it asap until it is finished.