Each ship has up to 3 Shadow Missions. The objective for the current mission can be seen in the Mission Bar in the Hangar. Below, you can see that the Mosqutio's 2nd mission is to destroy 15 Spider Bosses.
Each mission is worth a number of stars. Completing missions earns stars and, in turn, Shadow Rank promotions.
Death Penalties
If you die during a shadow mission, you will lose some of your progress in that mission. Below are the types of mission and their penalties: Destroy 'x' small ships of type 'y' 100% Progress Lost
Destroy 'x' big ships of type 'y' Lose 2 Kills
Destroy 'x' bosses of type 'y' Lose 1 Kill
Score 'x' points in 1 track 100% Progress Lost
Accumulate 'x' points Lose 1 million points
Complete 'x' tracks on 'y' difficulty Lose Current Track
Collect 'x' pickups of type 'y' 10% Progress Lost
Mission Restrictions
Shadow Missions have some restrictions. These are listed below. In general, songs with the Shadow Ops Icon next to them are appropriate for the mission.
Tracks with the Shadow Ops Icon can be used to complete the current mission
Destroy 'x' small ships of type 'y' Any mode. Tracks with Icon present
Destroy 'x' big ships of type 'y' Any mode. Tracks with Icon present Destroy 'x' bosses of type 'y' Any mode. Tracks with Icon present
Score 'x' points in 1 track Standard Mode Only
Accumulate 'x' points Standard Mode Only
Complete 'x' tracks on 'y' difficulty Standard Mode Only The track must be longer than 3m:30s You can play on higher difficulty if you wish
Collect 'x' pickups of type 'y' Any mode. Any track
Disabling Shadow Missions
You can toggle Shadow Mission progress on and off in the 'Game Settings' screen. When disabled, you will not gain, nor lose, progress for that play through.