At base level 80 a new quest will appear at Thanatos Tower called Rune’s Power that will unlock this feature. Alternatively, this feature will automatically unlock when you obtain a rune prior to this though you will still receive this quest when you reach level 80. This will most likely unlock automatically since most events and kafra adventure logs reward you with several runes.
If you have to complete the quest it leads you to Thanatos Tower. If you haven't been there before use a Kafra Girl to teleport to Yuna, then head to the east side of Yuno and talk to Karthaus the Airship Manager to go to Thanatos Tower.
Once here you should see a quest icon on your minimap that takes you to Montenega. If you do not see this quest ensure that you have Show All Quests enabled (see Questing and Filters ) in case this is preventing you from seeing this quest.
Once this feature is unlocked you'll obtain a rune box that's stored in your inventory.
Open your inventory and look for a round purple box near the top of your inventory. Use this box to open the rune interface.
Your rune box box contains 7 small nodes and 3 big nodes.
The node I’ve selected on the right is an example of a small rune which gives Crit Damage and Crit chance. These small runes can be upgraded to level 15 so these bonuses become quite large.
The node selected on the right here contains an example of a large rune. Large runes impact skills.
This rune gives me extra damage to Fire Pillar but adds significant damage absorption capabilities anytime I'm standing in these Fire Pillars under the Fire Guardian effect.
Large runes may also grant you new skills like wizards [Comet Crash] which casts a massive comet over a huge radius, much larger than meteor storm.
Runes are obtained from events, weekly content such as Thanos Tower, and can be purchased from the Rune Shop in Prontera every week.
To access the shop head over to the Rune Shop NPC Rainie in Prontera. You can only purchase so many each week (reset's on Monday's) and they come in several flavors. The Faint Rune Stones are B class runes which are green colored, Smooth Rune Stone are A class runes which are blue colored, and sealed rune packs contain smaller runes. Buying all of the large runes every week costs 1,750,000 zenny, quite a bit for a new player. You can also receive more of the small rune boxes if you exchange glow metals, contribution, or gold medals if you need.
If you can’t afford this don’t stress too much about this yet. Events will give you runes as well as the Kafra adventure book and with some luck you’ll roll a few for your class to get you some good bonuses. Even if you don’t roll any for your class you still have ways to force it.
Don't forget about these small runes though, they are very strong as they can be upgraded via the Upgrade tab of your Rune Box for significant stat bonuses.
Location of the Rune Shop in Prontera
Putting a large rune into your rune box is not enough to activate it. At the bottom of every large rune it will tell you the requirements to activate these runes. In the first below on the left, an ATK Rune, DEF Rune, and Buff Rune are required to activate it. This means the rune must be surrounded by one of each type of small rune. The second example shows that a DEF Rune, DEF Rune, and Unrequired are needed. This means two defense runes and any other type of rune.
This rune requires an ATK, DEF, and BUFF rune (Red, Blue, and Yellow)
This rune requires two DEF runes and any other kind of rune
Requirements are preset for each large rune. This means that a Fire Protection rune will always require an ATK, DEF, and BUFF rune, it's not random. You can change one of the requirements by using a "Carving Knife" via the Rune Smelting options but in my experience you do not need to do this as you can usually get things to work if you just move your large runes around.
You can sacrifice runes to roll for new ones directly from your Rune Box interface.
Smelting Options
You can use the following smelting options:
Advancement: Converts 3 large runes to a new large rune with chance to upgrade to higher tier. Used to upgrade B runes to A and A runes to S.
Directional: Converts any 5 large runes to a new rune for a class of your choice, which defaults to your current class
Attribute: Consume 3 of the same large rune to re-roll one of the same type with higher chances to roll good stats and increased chance for probability roll
Carve: Consume a carving knife (BCC item) to change the color required to activate a large rune
Replacement: Target a specific S rune and consume 3 S class runes for the class that the targeted rune belongs to receive the targeted rune. Use this to choose a specific S rune you need if you have a bunch for your class that you don’t need.
Most of the time you do not need to do rune carving to activate all your large runes. Just play around with them to find the right arrangement.
Smelting will be your primary source of obtaining S runes early on. Some runes are absolutely bonkers so this is very good to invest in once you have the zeny to do so, these go a long way for every job.
There are three more slots outside your primary rune tree where Arcane Runes can be slotted. These are not job specific and can become quite powerful. These runes can be obtained from the Whitestar Airship instance.
While you may slot three arcane runes you can only use two of the same color at any given time. This means you can either equip two yellow and one red, or two red and one yellow.
Arcane Rune Slots in your Rune Box
Each rune grants you 1200 Base HP as well as one additional stat which you can increase with drops obtained from Whitestar Airship. Starshine sand upgrades your rune's current level, while the Holyglow Crystals increase the maximum level of the rune.
Increasing rune level using Starshine Sand
Increasing max level using Holyglow Crystals and Zeny
Every rune requires the same amount of dust, crystals, and zeny in order to max them out. Below is a table that shows the amount of dust and crystals per level range, as well as grand totals.
The higher levels of Whitestar Airship are incredibly difficult and require specific classes to clear consistently and even then, RNG for the week may be awful forcing you to bring down the difficulty slowing your progress. Each rune will take months of effort to maximize so try to spread your upgrades among your most important arcane runes since the costs increase very quickly.