The Subterra is the underground, lower areas of the Pharos of Ridorana. They cannot be accessed until after you have completed the First, Second and Third Ascents of the Pharos and destroyed the Sun-Cryst.
Once that section of the story is completed and you have returned to Balfonheim Port you can access the Subterra by warping back to the Pharos at Ridorana and using the Dias of Ascendance to access a floor called Penumbra.
The Subterra is actually made up of four distinct floors:
(Click on the map to enlarge)
At the start, you will only be able to access Penumbra using the Dias of Ascendance. In order to access each of the other floors, you will need to find four Pedestals of Night on each of the floors and load them up with 
Black Orbs, similar to what was done on the First Ascent of the Pharos of Ridorana.
The Black Orbs drop from enemies killed in each of the corner rooms of the Subterra.
The round, ‘main’ areas of each of the floors are packed with enemies that will continue to spawn, so quickly make your way to one of the corners. Once you reach the corner, you will notice that it is completely dark.
You will have to slowly fill the Pedestal of Night in the corner with Black Orbs to cause it to light up. Here are the number of orbs you require for each of the Pedestals of Night:
| Floor | Northwest | Northeast | Southwest | Southeast |
|---|---|---|---|---|
| Penumbra | 9 | 18 | 6 | 3 |
| Umbra | 9 | 15 | 18 | 15 |
| Abyssal | 21 | 15 | 12 | 27 |
The game will give you the option to add 1, 5 or 10 Black Orbs (if you have them) into the Pedestal of Night. Be careful not to overfill the pedestals as there is no way to retrieve Black Orbs if you go over the required amount.
Another helpful hint is to return to the Pedestal of Night and regularly fill it with Black Orbs. You do not have to fully fill the pedestal before it will begin to light up the room which will make it significantly easier to navigate.
In order to reach the Unknown area, you will need to search for and defeat Phoenix somewhere in the Subterra. It can spawn on any of the floors but is not usually hard to find as you will naturally encounter it while searching for Black Orbs.
Level: 55
HP: 92,522
Steal: Windslicer Pinion (55%), Eye of the Hawk (10%), Split Armor (3%)
Phoenix is not hard to defeat. You will need to use ranged attacks, Magicks or the 
Telekinesis to damage it. Make sure to buff your party members in advance of initiating the battle with 
Protect, Shell, 
Haste and 
Bubble and to keep Phoenix attacking your tank by using Decoy. You should also set up a Dispel Gambit to remove Phoenix’s status enhancing spells.
There are two other Marks that are fought in the Subterra:
Ixion can be spawned on any of the three floors of the Subterra. You must travel using the Dias of Ascendance down to one of the three floors.
Penumbra has the lowest chance, then Umbra, then Abyssal and Ixion will have lower HP if it is spawned on Abyssal, so your best bet is to clear all the way through the Subterra before trying to get it to spawn.
It has a small chance of appearing every time you take the lift from the main level down though, so it may spawn on you during any trip to any of the other levels. You will know that it has spawned because there will be no other foes in the area.
Just wait around for a short period and it will appear. Check out the Ixion area for more information on how to defeat it:
The last Mark in this area is the Shadowseer which is located in the Unknown area of the Subterra, so you will have to have completed all of the Pedestal of Nights and filled them with Black Orbs.
You will also have to seek out and defeat Phoenix in order to reach the Unknown floor. Take the Dias of Ascendance down when you are ready but be cautious – the battle begins as soon as you arrive.
This is everything that you can do in the Subterra.
