Metal Gear Solid: Portable Ops/Metal Gear

Now that you know that Metal Gear is involved (for real this time, it's not the Shagohod), you will need to find where the nukes are stored. Put spies in the Security Base if you didn't get the report Classified Information.

Security Base
There is a Body Armor located in the Floor B1 to the west. Then, go retrieve the Secret Document upstairs to the East.

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). Having Thermal Goggles could help, and also some TNT (you can also find TNT in the mission, in a crawling space). You could also bring with you the Body Armor and some ammo 7.62MM T or 9MM T.

Warhead Storage
There will be a Boss Fight later in this mission. But first, you should have Snake equipped with at least Thermal Goggles (developed by your Tech Unit), either the Mk22 or if you're a demon a lethal weapon (a Mosin Nagant can also be found in this mission, crawl under the lasers to get it), ammo for your weapon and perhaps the Body Armor. Then make your way until you can bomb the objective, there will be a cutscene. And the Boss Fight.

Map
If you didn't receive the Airport Located report, put spies in the Warhead Storage and then wait or do a mission.

Airport
You will need to find a Government official and interrogate him, he's located on the last floor.

Silo Entrance
You will need to find the Silo Entrance. There is an RPG on this map. When you approach the objective, there will be a cutscene followed by a Boss Fight:

When the battle is over, there will be a cutscene.