This mission should go smooth until you infiltrate the HQ. When you get there, go to the basement. Here's where you find all the 3 clues to continue with this mission:
The dead body
Computer in the same room
The computer next door
Now proceed to the church. There are another 3 clues here:
Blood on the floor
Bullet Hole on the floor
Hole in the Wall, next to entrance
Now you can determine the trajectory and go to another church. Once you get there climb on top of it. Use the scout ability to highlight the climbing areas.
Once at the top analyse the floor. And follow the footsteps down...