The base - after the first couple of missions you finally have access to your command base. This is where you prepare and gear up before missions.
Tactic room - information: this section gives detailed background information of your original squad as well as other 3rd party organizations.
Stock - trade: meet up with the local Seeker (Trader) and trade weapons, ammo, vehicles and other gear!
Garage - equip: equip your vehicles with weapons, ammo and gear or stock up items from the previous mission.
Garage - repair: vehicles damaged from the previous mission can be repaired here. There is time limitation on how many can be repaired.
Garage - armor: upgrade your vehicle's armor to make it more durable. Limited time slot for each vehicle armor upgrade.
Lab - hormone treatment: increase the heath stat of your soldiers. Upgraded health bars will show as a white bar in comparison to the standard green bar.