Annihilation operations are distinguished from other operations by the following unique mechanics:
- There are 400 enemies (excluding allies and bonus enemies) and the player is given 10 Life Points; this can cause the Annihilation operation to take a very long time to be cleared.
- In the event the player loses all 10 Life Points, the Annihilation operation will be cleared instead of ending in a failure; this also occurs if the player quits the operation.
- When an Annihilation operation ends, the Sanity is returned relative to the amount of defeated enemies. Rewards are scaled to the amount of defeated enemies; the more enemies defeated, the more rewards given.
- The automatic DP generation is disabled and the maximum DP count is increased to 999. This means that using Vanguards are the only means to generate DP in Annihilation operations.
Annihilation operations are the only way to earn Orundum aside from trading and rewards from missions and events, but the maximum amount of Orundum one can earn from Annihilation operations in a week is limited.
The Fan Appreciation Event update in the Global server introduced a rotation system to Annihilation operations, which divides them into three categories: Permanent Missions, Rotating Mission, and Hypothetical Targets.
- Permanent Missions are always available, which includes the three original Annihilation operations.
- The Rotating Mission is available for a certain period of time. Once the Rotating Mission ends, it is moved into Hypothetical Target operations and a new operation is introduced in its place.
- Hypothetical Targets include the out-of-rotation Annihilation operations. One of the Hypothetical Targets is available as the Simulation Mission for a period of time.
- Unlike Permanent Missions and the Rotating Mission, the Simulation Mission does not award Orundum and Battle Records when cleared despite still costing Sanity to run and having the exact same Sanity return/reward rules. As such, running the Simulation Mission is only relevant if the player has not claimed its one-time rewards during the time it was a Rotating Mission.