You may purchase faction upgrades by spending Faction Points. These upgrades are then "powered" through a daily expense of faction Honor.
Faction upgrades are extremely useful, as they will grant your membership access to certain facilities that they may require (such as a Medical Bay, or a Forge for use in crafting). Or they may provide your faction with extra protection (such as more powerful Stronghold Wards). Additionally, there are a large number of "flavor" upgrades that simply change the way your Stronghold appears.
Your faction will accrue Honor and Faction Points through various activities performed by its members (see the Honor page for more information).
If your rank within the faction allows you to "edit" the faction (e.g., you have the highest possible permissions), you will see a new tab on your faction's profile page labeled "Faction Store". From here, you can browse the list of available faction upgrades.
Each upgrade has an associated "Faction Point" cost. If your faction does not have sufficient banked Faction Points, you will be unable to purchase the upgrade.
Every night, your faction will be forced to pay a number of Honor points for the use of each upgrade it has active (note that flavor upgrades do not incur a nightly charge). The number of points required varies but is usually 1 per upgrade. This cost will only be paid if you have a Stronghold.
If your faction is unable to pay the upkeep cost for the upgrade, it will be disabled.
If you have the "edit faction" permission, you can selectively enable or disable specific upgrades (in order to avoid paying the upkeep cost). This is done through the "Upgrades" tab on the faction profile page.
Upgrades can be enabled or disabled at any time. However, enabling an upgrade will immediately force the faction to pay for its upkeep cost.