I know there are many topics about this glitch, but none of them answered the question; “How do you get a falcon without Jun in it???”.
The game has not been patched (like some has earlier suggested) because I got it to happen only once LAST NIGHT, but the elites blew up the falcon before I could emp it. 
After that I tried many times over and over again, and Jun kept on flying it, so I couldn’t hijack it.
Does anyone have the answer to this, or is it truly just a random thing that happens every now and then?
In my experience, it is a combination of going really freaking fast through the level, and a bit of luck.
Try not to kill any of the enemies in the first area (overlook) except the two Grunts off to the left side if you want to grab a PP there: they seem to be safe. You need to get through the level and trigger the Falcon to fly over SPADE area before the one with Jun in catches up.
I sometimes can’t get it either and I’m the speed run record holder on 3 difficulties!
Thank you for the tips. At which point exactly do you trigger the falcon? Which one is the SPADE area? It’s already too late at the point when you first encounter the covenant because Jun is already fighting them from the Falcon at that moment. So, it has to happen before that.
> Thank you for the tips. At which point exactly do you trigger the falcon?
I’m actually not sure.
> Which one is the SPADE area?
You know the truck you get after the Overlook area? That truck is called a SPADE.
> It’s already too late at the point when you first encounter the covenant because Jun is already fighting them from the Falcon at that moment. So, it has to happen before that.
I actually don’t understand it myself, I just went through the motions enough and it worked.
Really, the level is so easy anyway that you shouldn’t bother unless you are speed running or want to break out of the level for fun.
Cody Miller’s Legendary run is what I based my stuff on.
Thanks man. I’m just doing it for fun. I’d like to explore the second part of the broken bridge. 
I did it last night. Started up from rally point alpha, and on the first try June wasn’t in the Falcon, I was able to emp it without any trouble. It seems like the chances are higher when you start from rally point alpha then when you sart at the beginning of the mission. It was a blast exploring the other side of the broken bridge, and going to the top of those mountains.
Thank you guys for your help.