Metal Gear Solid: Portable Ops/Welcome to San Hieronymo

The game begins with a cutscene where Snake wakes up in a Prison.

Comm Base
You will then return to the Map. You will need to head to the Soviet Patrol Base.

Soviet Patrol Base
After you've unloaded from the truck, just walk a bit until a cutscene plays. Then, make your way into the building to retrieve the Secret Documents.

First Recruit
Now, choose any of the map locations and find a soldier, incapacitate him whether it's with your Tranquilizer Pistol or with your bare hands and bring him back to your truck (you can drag bodies by maintaining psx: S). There will be a cutscene and you will return to the map.

Comm Base
You will need to return to the Comm Base. After you've contacted Para-Medic again, you'll return to the map.

Hospital
You will need to at least visit two of the marked spots. After that, you'll need to head to the north building upstairs.

Research Lab
You will first need to head north to get a cutscene. Then go to the building directly south of where you are for another cutscene.

Spy Unit
You know that you have to go to the Harbor, but you don't know how, Campbell suggests that you put men in the Spy Unit affected to the Supply Depot, do so and wait 12 hours (ingame).