In the game ships are organized into fleets. Fleets move, engage in Tactical Combat, and perform actions by assigning them missions. The fleet will travel from it's assigned base to the mission target, perform the mission and return to base. This automation reduces the tracking of individual fleets for new missions after they've scattered across the star map.
Selecting a Mission
Missions are selected by right clicking on the system to target the mission or, with certain mission types, by right clicking on the fleet to target the fleet to perform the mission.
Each mission will take a certain number of turns to complete. If a Fleet does not have enough endurance to travel to the target and complete the mission, that fleet won't be able to take the mission. Please see the Fleets page for more information on fleet endurance.
The details of a system are unknown until a fleet has fully surveyed the system. This will reveal all the planet statistics and if playing the human faction, all nodelines leading to the system.
Requires: Colony ship
The fleet will ferry colonists and materials to a new world in order to claim it for your empire. The fleet will continue to transfer between base and the colony site until it becomes self-sustaining. Once the colony is self-sustaining and the colonizing fleet has returned to base you will be given the option to have the fleet continue supporting the colony and increasing its rate of growth, or completing the mission. The more colony ships you have in your fleet, the quicker the colony becomes self-sustaining, the quicker the planet is terraformed and the quicker the infrastructure is completed.
This mission will move the fleet to a new base. Note that colonies can be fleet bases but are never as effective as a Naval Station.
Causes the selected fleet to patrol a system for the duration of endurance, engaging any fleet that enters the system with a chance of interceping fleets in nearby systems. "Nearby" is defined as reachable in one turn. While on a patrol mission, a fleet’s Admiral will have an increased reaction time, as being vigilant is part of their mission. In practice, this gives the Admiral a large bonus to intercept enemy fleets approaching nearby systems. Probability of interception = Admiral's reaction stat + patrol bonus. Hivers are capable of intercepting via the gate network.  
The fleet will blockade the system to intercept any enemy ships attempting to enter or leave the system but the fleet will not enter the system to engage planets, stations or enemy fleets already in the system. This will not intercept Hiver Gate Travel, but will intercept Hivers moving STL.  Interdiction will shut down trade in the targeted system.
The fleet will attempt to destroy all enemy fleets, defenses, bases and attack colonies in order to take ownership of the target system. Fleets using this mission will spend multiple turns in the targeted system, dependent on the fleets endurance.
The fleet will attempt to destroy a specific targeted fleet, colony, or station. Fleets using this mission will only spend one turn in the targeted system, regardless of the fleet endurance or the outcome of any combat.
Requires: Construction ship
Construct a Stage 1 station with no modules at the target location. At the start of the game this is in orbit around a colony but can be placed anywhere within any system with the right researched technologies. The more construction ships you have in your fleet dedicated to the work of building the station, the quicker the station construction will proceed. Fleets not "at rest" ie. just completed Survey mission, on Patrol or Returning cannot carry out Build Station missions.
Requires: Construction ship
Once a station has completed construction of the modules required to upgrade, a construction ship can increase the stage of the station by one. The more construction ships you have in your fleet dedicated to the work of upgrading the station, the quicker the station upgrade will proceed.
Requires: Hiver Gate ship
Move a fleet to the target system and deploy a Hiver gate ship in the system. The Gate is deployed into its own fleet, called by default GATE, and is usually placed in the system map in the quadrant closest to the system that the fleet gating arrived from.
The present Mission system moves the fleet containing the gate ship to be deployed via the existing Gate network to the closest available system to the target before sending the fleet on its way. This can result in the gate ship itself being deployed in a sub-optimal location.
Requires: Loa ~4640 Cubes per NPG deployed
Move a fleet to the target system and build a Neutron Pulse Generator (NPG) in the system. The NPG is deployed into its own fleet, called by default ACCELERATOR FLEET, and is usually placed in the system map in the quadrant closest to the system that the deploying fleet arrived from.
The fleet may also optionally deploy NPG accelerators along the path taken to the target system. Given the FTL method utilised by the Loa, there is usually no reason to deploy an NPG any less than every 8 light years, though some folks suggest every 11 light years instead.
The present mission system does not take into account the existing accelerator network, instead moving the deploying fleet directly from its current location to the target system. This means that in order to extend an accelerator network, you must first manually assign the fleet to the closest star system yourself with Relocate before assigning the fleet to the Deploy NPG mission.
Presently the Deploy NPG mission is not available to fleets not at 'rest', thus if a fleet has just completed a Survey mission or is on a Patrol mission, it is not eligible for a Deploy NPG mission. Consequently, the current standard for expansion is to relocate the desired fleet to the closest NPG enabled and colonised system to the target system, use Deploy NPG to get the fleet from there to the target system and then use Survey with that fleet once the NPG is deployed.