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Not totally sure which bit you are at, but if it is the bit where you see the guy in the tunnel and he runs away as you try to shoot him, then it is really important you kill him quickly. If you kill him quickly the guards at the station are not alerted and you can travel through that station without even having to engage in combat. The first time I did it I killed the running guy a bit late and they massacred me at the station, the second time I killed him first shot and not a shot was fired at the station. Not totally sure if this is where you are talking about though.
Shooting that first guy you encounter (when you're told to kill him by one of your allies) makes a huge difference in the beginning of this section. Doesn't really make sense, since you'd think your big ass mounted gun would alert anyone nearby. Especially in a tunnel that would probably echo a fart, but oh well.
I got lucky and killed him from afar during one of my replays, and I was all tensed up for another heavy gunfight in the tunnel but we ended up practically driving straight through without much trouble.