From AliensRL Wiki
Missions are the AliensRL equivalent of quests: you are told to do something and then you do it. While a current mission is active, certain events can occur that will only be disabled when the mission is completed. While there can be direct and indirect benefits upon successfully completing a given mission, others are necessary to win the game.
In the current version of the game (0.8.2), there are only two mission, both of which are absolutely required to finish the single victory route. Later releases will introduce many more missions, some of which are class-specific.