Covert Missions are assignments you send squads to complete for rewards. The building requires Base level 8 and has one level. Mission quality and available squads determine what you can work on afterward.
How assignments work
Deploying a squad occupies one of the available assignment slots. If all squads are deployed, the game asks you to unlock more before sending another. Its unlock prompts point to the 2nd or 3rd Squad, or the Monthly Pass's extra slot.
Missions can attract raids from other players. Alliance membership also allows you to assist allies with their Covert Missions.
Mission quality and refreshes
SSR or higher missions can provide Treasure Map Shards, which can be exchanged with alliance members. Refreshing changes the mission list, and the game warns if doing so would remove unfinished UR missions. Those missions are lost from the list rather than carried into the refreshed selection.
The Alliance Center opens the membership needed for alliance assistance. The Squad buildings concern march availability; their level upgrades are separate from the quality of a Covert Mission.