The last thing you need to do is to leave the Mother Base. Turn on the iDroid and select the Missions menu. Choose the Helicopter menu and then order it to Pick you Up. Select the only airstrip available and wait for the helicopter to come.
During your flight you may notice that a new iDroid menu has been unlocked. From this menu you may run your Mother Ship from a distance and select a new mission. You may already see that the game has unlocked three new main missions. 3rd mission - Hero's Way, 4th mission - C2W and the 5th mission - Over the Fence. You may find it's description on the next pages of this guide. You may complete them in any order you like. From this moment on you may also choose to replay some missions you have already completed if you want to, for example, complete some skipped side quest or achieve a better rank.