There are two types of Missions: task-based Missions (Base) and time-based Missions (Daily, Alliance, VIP) which, upon completion, give a number of rewards, ranging from Power and Commander XP to Resources. Time-based missions are refreshed every 6 hours, and any incomplete missions are replaced. Missions can be completed anywhere within a few minutes, to a few hours depending on the type of mission. When a reward for a quest is ready to be collected, a green check mark will be shown next to each type of mission.
You can read more about the Base Missions here.