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. After this mission, head to the Comm Base if you want to recruit Para-Medic.

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) or do another mission.

Supply Depot
You will need to find the Secret Documents, after this the mission will be over.

Rail Bridge
You just need to reach the objective. Then when you're back at the map, put spies in the Supply Depot, the Research Lab, the Town and in the Soviet Patrol Base. Then either wait or do another mission until you receive Spy Reports about the diversions.

Supply Depot
There is only one truck in front of you with a guard patrolling nearby. Blow it.

Research Lab
You will have to bomb the culture tank, but, in fact there are two marked spots on the map, and each one is more like a big computer/machine. Just blow either of them.

Town
There are 3 trucks stationed in the Town. Two in the area in front of you, one up some stairs.

Soviet Patrol Base
You will need to blow up an armory located in the southeast, with a guard standing in front of the door, you can approach him from the side without being detected.

Rail Bridge
When you return to the Rail Bridge, if you've done every diversion mission, there will only be 3 soldiers patrolling, just join the target location. Do not go to the Harbor yet!

Harbor
You will have to infiltrate the boat, but first, retrieve the Cardboard Box located on top of the Boat (enter the boat, then head upstairs). Head downstairs for a cutscene.

Preparing for the next mission
The next mission will be different from the others, you might want to save beforehand, but also be sure to arrive equipped (with Non-lethal of course).