For the chapter of the same name, see The Lunar Sanctum (Chapter).
The Lunar Sanctum cannot be seen by humans, so Arlon doesn't need to worry about them. However, it is equipped with many defenses, including "a weapon so lethal, it makes Reset Bombs look like firecrackers." This is presumably the huge blue weapon that resembles a cat's eye, but this can also refer to the Chaos Kin. In addition, there are many lasers, and gates that can lock out intruders. There are also many troops from the Forces of Nature there, including Nutskis, Bladers, and, Arlon's favorite, Flages.
Before the events of this game, Viridi and the Forces of Nature captured an unspeakably evil being called the Chaos Kin. The Lunar Sanctum was built as a prison for the Chaos Kin, outfitted with many defenses. Viridi entrusted Arlon to watch over it. During the events of Uprising, Palutena and Pit stormed the Lunar Sanctum, unaware that if they destroyed it by beating Arlon, they would release the Chaos Kin. Unfortunately, they did just that, and Chapters 18-21 are spent trying to stop the mess that happened at the end of the Sanctum's life. After defeating the Aurum, Pit awakens as the Ring of Chaos.
The Lunar Sanctum Control Center powers some of the Sanctum's defenses and the enemy replicas. Pit faces it as a miniboss in Chapter 13, along with Dark Pit. The Control Center is a blue sphere. Pit should defeat Dark Pit first, as the Control Center doesn't attack until fired upon. When preempted, it will shoot a counterattack beam. Pit must dodge right away to avoid being hit. Once Pit defeats the Control Center, enemy replicas stop appearing.
A moon-inspired temple ruled by Arlon the Serene. Normally it acts like a new moon, hidden in the night sky. But when Palutena discovers it, it shines like a full moon, opening up to fire a devastating laser at Pit.
Lunar Sanctum Control Center
One of the cores required to control the Lunar Sanctum. Destroying it would disable the sanctum's camouflage and other defenses. To prevent this, Arlon the Serene tricks Dark Pit into defending the core.