Mission 1 -- Communication Breakdown
Secret 1: At the beginning of the mission, you'll need to take out the two guards next to the ruined shed. After killing the second guard with your thermal sight, head into the shed. The secret will be next to the generator.
Secret 2: When sneaking under the docks of the large building, you'll jump up onto a ledge and be demanded to kill the enemy standing directly in front of you. The secret will be to the right of the enemy beneath a staircase.
Secret 3: After detonating the explosives, head into the building to the right of your escape path. The secret is up the stairs on your right next to a few guards.