Mother Base is your home away from the battlefield and has a few main functions in the game. It is first unlocked after completing Mission 2 and one of the first functions (and probably the main one) you learn is Fultoning soldiers from the battlefield and assigning them to the various platforms on Mother Base.
There are only a few that are open at the beginning, but as you progress through the main missions, more platforms will open up. Each platform has a specific function tied to it, like the Intel Platform helping you out in the field by providing information, such as general enemy locations when you get close enough, or talking about when the weather will change.
As previously mentioned, Mother Base starts out with only a few platforms available and each one has a unit attached to it. Fultoning enemy soldiers and prisoners in the battlefield will contribute levels to those units, unlock various functions. Of course, you only have so much room on your platforms, which you can extend by building add-ons.
When you access your iDroid, you can head to the Mother Base tab and you'll see one option that says Base Facilities. Choose this and you'll be brought to a screen with a list of all of your platforms. In order to upgrade these, you will need the proper amount of GMP and resources. There are two types of resources, processed and unprocessed.
To use the functions, such as upgrade your platforms among other things, you need to have processed materials. You can find some in most locations on the maps, however, these small containers only give very small amounts. That's where your Base Development Unit comes in, as they will find resources, but they will be added as unprocessed materials. They will also, over time, handle the resources and make them into processed ones.
As you go along in the game, you will eventually unlock an upgrade to your Fulton Device that allows you to capture vehicles. This upgrade also allows you to capture large containers, which contain a lot of unprocessed materials. There is a trick in the game, where you can farm a lot of these containers in three particular missions. Check out the Farming Resources page for more details on that.
Personnel and Skills
Every single person you extract via the Fulton Device back to your base will have a letter rank assigned to each of the units. These values are hidden from you at the beginning of the game, but as you upgrade your Int-Scope, you will be able to see these values. However, the upper limit only goes so far, requiring more upgrades to be able to see the top-tier troops (S++).
Another thing you'll be able to see once you've upgraded your Int-Scope is that some enemies might have skills. These skills are always hidden from you, but they generally fall into one of three units, Combat, R&D or Medical. While the majority of the skills are beneficial, there is one noteworthy one that isn't so useful, the Troublemaker . Personnel with these skills will end up causing trouble for your crew, so it's a good idea to dismiss them, unless they have very high stats.
Note: There are two ways to quell the Troublemaker skill, besides dismissing them. The Diplomat skill helps, but placing two Troublemakers in a unit will also do the trick.
Forward Operating Bases
The Forward Operating Base (or FOB) is an extension to the Mother Base that will unlock upon completing Mission 22. This can only be accessed while you're playing online, so going offline will make it so you can't make any adjustments to the FOB. You can invade other people's FOBs and people can also invade yours, where you'll be alerted if you happen to be online at the time.
The first FOB you get is free, but subsequent ones will require you to spend Mother Base Coins. You may receive some from the daily rewards system, but you can also spend real money to purchase more. The FOBs will allow you to upgrade your platforms further in conjunction with the offline versions, meaning you'll be able to have more personnel and higher levels.