Forty sixth mission of Metal Gear Solid V is in fact its true ending. Enabling it isn't quite easy, as you will have to meet up with several requirements which are listed later in the text.
The very first thing you will have to do is completing the most important side tasks. Finish all of the missions form the first act (1-31). As for the second act you only have to finish completely new missions, this is: 32 (To Know Too Much), 35 (Cursed Legacy), 38 (Extraordinary), 41 (Proxy War Without End) and 43 (Shining Lights, Even in Death). You don't have to take care of the main mission 45 (A Quiet Exit) as it is unlocked separately and finishing it is not necessary to unlock task nr 46.
Apart from the main missions, take care of all of the Important Side-Ops marked with yellow colour. Specifically mission 143 (Extract the AI-Pod) and missions 145-149 (Search for the Escaped Children 01-05).
Another thing you are required to do is listening to all of the major tapes. Tapes can be played with the iDroid. After activating it, go to the Missions tab and then Cassette Tapes. Play all the yellow tapes. In fact you don't have to be listening to them from start to the end. You only have to make the dots by the titles disappear.
Listening to these tapes comes with a complicated task you will have to deal with. You will have to exile scientist Emmerich from the Mother Base. In order to do so however, you will have to acquire the tapes from Questioning Huey, specifically numbers 1-6 (categories are marked on the picture nr 1), these are the tapes that question the intention of the scientist. The tapes can be found by finishing the following missions:
- Questioning Huey 1 - Finish mission 12 (Hellbound).
- Questioning Huey 2 - Finish mission 13 (Pitch Dark).
- Questioning Huey 3 - Finish mission 143 (Extract the AI Pod).
- Questioning Huey 4 - Finish missions 145-149 (Search for the Escaped Children 01-05).
- Questioning Huey 5 - Finish mission 43 (Shining Lights, Even in Death).
- Questioning Huey 6 - Listen to the tape "Reasons for Facilitating the Wolbachia Mutation 2" from the Questioning Huey 5 group when having D-Dog selected as your active Buddy.
After you finish listening all of the tapes, go and complete some missions. After finishing couple of them, you will be called by Miler to the Mother Base. The cutscene will start (picture 2).
If the mission 46 is not unlocked despite completing all of the mentioned steps it means that you will have to upgrade the Mother Base platforms more. In order to upgrade them, use the iDroid and select Base Facilities tab. Example of the upgrade screen is depicted in the picture above albeit your base doesn't have to be upgraded that much. You will need to acquire 2-3 level of the platforms.
Important Note! - You will have to have a lot of cash in order to upgrade your base. If you don't have enough money, earn it by completing more missions and dispatch your subordinates. A single upgrade may also take up to several hours, which is also an important thing to remember.
Important Note 2! - Along with the mission 46 the following missions 48-50 should unlock automatically. They're very similar to the previous tasks and you don't need to complete them just yet.