Missions
Missions are essentially the goal of the ship and the crew, much like other code bases (except no one really pays attention to those objectives anyway). Completing the assigned mission is what ends the round. Note that more missions may be added to your ship objectives upon the completion of your past mission.
 Missions on FTL13
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Kill Mission
This is the mission you can expect to see the most. Basically the goal here is to destroy a certain number of ships and await further orders once complete. It may be a good idea to read this.
Destroy Syndicate Vessels
The Syndicate have made bulked up their army of ships, which is normal, except now they've really bulked it up. It is now your mission to thin the herd, how your crew does it is up to you.
It may be a good idea to buy extra MAC rounds for this, since you don't quite know what ships you're going up against. A Ravager can be expected in thick patrols.
Eliminate Pirates
SolGov has been having some trouble with their settlements being attacked by pirates. Since there isn't much else on the board suited for your ship, you'll have to clean it up. This is more of a favor than an "act of kindness". Still, do not attack SolGov vessels.
Pirates are hard to find. If the mission is going too slow, adminhelp it.
Fetch Quest
This mission entails going to a specified system and retrieving an item of interest. How you get there is up to your crew but going around Syndicate systems is boring as all hell stop going through SolGov/Neutral systems you butt. You can be sure that whoever you're stealing from rightfully procuring from will be PISSED upset and may send a battalion after you.
Syndicate Documents
Our intel team has pinpointed an area that most likely holds very important and sensitive documents belonging to The Syndicate that they're probably better off without. Your ship is small enough to avoid getting the big dogs called on you, at least before you steal the documents. The documents are well guarded and a lot of backup is bound to be called when they find out you're the ones who stole them. Good luck!
Decommissioned Weapon
One of our weapons has failed testing and your ship is the most available to get this thing out of here and back to head researchers. The location of the weapon and the destination it's meant to go to are included in the mission details. Careful, though, since The Syndicate may want to get their hands on this for whatever ill-willed scheme they hatch on a daily basis.