There are 2 main sectors, with 10 missions per sector in the game.

 

As you progress, each sector will increase in difficulty until you reach the last sector.

 

The final sector is the most difficult and is the ultimate reason for being a Star Commander in the first place: Boss fight.

 

Bad news: If you make it to the last sector but fail the mission, you will have to start over in Sector 1.

Good news: Your permanent upgrades will remain!