An important part of being battle ready is knowing how to evade your enemies. J.A.R.V.I.S. will help you avoid potential threats, so be sure to listen closely to his instructions.
When J.A.R.V.I.S. tells you to move, carefully sneak forward.
When J.A.R.V.I.S. tells you to stop, freeze.
J.A.R.V.I.S. will tell you when it is safe to move again.
If you don't freeze, you will be detected and will have and will have to start the mission over.