At the Third Echelon HQ there are some guards giving me trouble. I tried to get past them many times and always got killed before reaching the checkpoint.
I'm referring to the guards that you see after going up the elevator and talking with the assistant.
For this sequence, speed is of the essence, which is somewhat atypical of the rest of the game, where careful consideration is generally rewarded. You have a little bit of time to react to these guards before the shutters close, but not really enough to have an extended shootout.
The easiest way to win, especially on consoles, is to bring a pistol that has been upgraded with a laser sight. I personally prefer the Five-Seven. With a laser sight, your weapon will tend to enter the "aiming" state centered on an enemy's head. This means you can rapidly take several guards out by looking in their general direction, entering the "aiming" state and quickly taking a shot.
The Five-Seven also has an integrated silencer, which means that in many cases you can kill several enemies without being detected with this method. There's a range past which this auto-aim trick doesn't work properly, but in this particular case you should be close enough range to take these guys out.
Otherwise, just be prepared to move quickly down the hallway, shooting at one or the other guard - this is usually enough to stun lock them, if you don't get lucky enough for a kill. You should be able to close the distance and finish both of them off before the gate closes.
Finally, if this isn't helping - go loud. Use something explosive or a primary assault rifle/SMG weapon if you have one. There aren't many guards who can be alerted in this area, so there's limited penalty for breaking stealth.
You now need to make your way to the elevator. Up through the ventilation shaft and into the car park again. Just opposite where you enter the carpark is another surveillance camera. Watch its movement and move to the right toward your objective marker when the coast is clear. Don’t go up the ramp otherwise you’ll alert the guard. Activate the lift and when it stops move toward the 3rd Echelon reception desk. Talk to the receptionist. A cut scene will kick in. Get ready! You’ll only have a certain amount of time to escape before the shutters come down on you and you get caught. Jump over the desk and go straight ahead veering left down the corridor. We recommend that you just run down the corridor toward your objective marker before the shutters come down, take out the guards with your weapon. Follow the objective marker toward the server office, stop just before the corridor veers right.
We recommend that you just run down the corridor toward your objective marker before the shutters come down, take out the guards with your weapon."
Direct approach just didn't seem to work for me, and I found it weird that stealth wasn't even possible. Later, I found (via) that there is a stealth approach - go through the railings behind the office assistant.
