Mission Rewards
Special Items
Some items that are used or gained from missions are put in the "Special" tab under the Trade menu. They are explained here:
Blueprints
They allow for special buildings or modules to be constructed. Known blueprints include Anti-Resistance Base, Exotic Turret, Exotic Barrier, and other Exotic structures/weapons.
Complex Tech Parts
Complex Tech Parts can be gathered by scrapping Artifacts that have been dropped by a NPC or have been collected from a mission. They can also be gained by opening Base Crates acquired from raiding level 4 bases.
You can find the amount you have within the Special Tab which is under the Trade Tab
CTP is often used by many player-to-player Trading Groups, outside of using the Trade Center, as the standard currency for trading in Artifacts.
Corruption
Acquired when using the Deeper Bond ability of the The Oruas Eye (ally) or when completing a daily mission when the ally's Vision of Duty effect is active. Each corruption takes up 500 space in cargo, but can be spent in the Corruption Market.
Exotic Matterhttps://galaxylegion1-1faae.kxcdn.com/images/icons/special/exotic.pngEM
Exotic Matter 
EM is a rare substance which can occasionally (in actuality, considering the size of most mineral shipments, pretty frequently) be obtained through typical mineral shipments. It is used as a resource to complete certain missions, similar to energy, but otherwise has no functional purpose. This is a fairly useless material at lower levels. Most useful if given to a friend (assuming the player is not in immediate need of the materials), unless you have started working on the very high level missions.
It is suggested that the odds of getting EM in mineral shipments rise considerably when the player is at or above a certain rank (rank 85 and higher?), but this has not been confirmed. (This part is written by Joseph4) "I have recently reached level 85, and I noticed a BIG increase in the Exotic Matter and other rare minerals I was getting per shipment."
NOTE: Certain extremely high level missions unlock blueprints to weapons, defenses, and resource production structures that are created via the use of Exotic Matter. For example, 400 Exotic Matter, when used with the corresponding blueprint, can build an Exotic Turret, which gives 250 planet attack. This actually makes exotic matter an incredibly useful commodity at the high levels, especially with the heavy Exotic Matter requirements that some missions have.
Exotic Matter EM is also needed for upgrading a Legion base, making it even higher in demand.
Along with Kurenite, Exotic Matter was once used by many Trading Groups as the standard currency for trading in Artifacts. 10 Exotic Matter equals 1 Kurenite. 10 Kurenite equals 1 Complex Tech Parts.
Raix
A precious substance available from The Tejiar Reformation daily mission for use in the Raix Market. (forum topic)
Political Favor
Unlike Exotic Matter, which only really comes into its element in the higher levels, Political Favor is incredibly important very early on, continuing throughout the game because the Fourth Tier upgrade is the Soldier Outpost, a very important building which can make or break the defense of a planet. Many people burn through Political Favor quickly and place Soldier Outposts frequently.
You can get political favour from completing certain missions. Look for missions that have a reward that looks like a yellow crown.
Prejoran Tech 
PT
Technology belonging to an ancient race known as the Prejor. Required for building special modules related to, or of, Prejor origin. Obtained from Prejor related missions. http://galaxylegion-erismedia.netdna-ssl.com/galaxylegion/images/icons/special/relic.png
Prismodyne Energy
Prismodyne Energy is acquired from each completion of the daily mission Porowyn's Arrival. Each Prismodyne Energy takes up 1,000 space each, but can be spent in the Prismodyne Energy Network Market.
XTS-9
XTS-9 is an extremely toxic substance that is used in experimental industrial production. There are various high-rank missions that require XTS-9. Producing it is dangerous.
Zolazin Debris
Debris collected from battles with Zolazin NPCs. Required for a mission involving the Zolazin.
Tier Items
Mission tier items are gained through the FULL ending of the required number of missions. Note that what mission is ended does not matter, only the total number ended.
Also note that these are missions ended, not completed. Most missions require more than one completion before they end forever. In other words, you have to do a mission until it goes away (being replaced by another mission counts) before it is considered to have been "ended".
Unless otherwise specified, all mission tier items require NO space on a ship. The following can also be viewed in table form on the Mission Tiers page.
3 Missions Ended - 1st Tier
Omicron Injector: Energy Charge +10 (Speeds up Energy Recharge by 10 Seconds), Added to Energy Category on Ship
6 Missions Ended - 2nd Tier
Harmonic Resonator: Shield Charge +10 (Speeds up Shield Recharge by 10 Seconds), Added to Defenses/Shields Category on Ship
9 Missions Ended - 3rd Tier
AI Supercomputer: Adds a 5 point bonus to scan, attack, defense, and cloaking, Added to devices category of the ship
12 Missions Ended - 4th Tier
Ability to construct Soldier Outpost on planets (size 3), providing Invasion Defense +300. Cost: 50,000 Credits and 5 Political Favor.
15 Missions Ended - 5th Tier
Prototype Mech XV: Provides 15 attack bonus during planetary invasions, added to weapons category of ship.
18 Missions Ended - 6th Tier
Thrust Stabilizer: Adds a 10 point bonus to defense, and 30 points to hull integrity, added to defense category of ship.
22 Missions Ended - 7th Tier
Q-Phase Battery Array: Multipurpose wave storage, boosting max shield and energy by 15
26 Missions Ended - 8th Tier
Gamma Channeler: Funnels incoming radiation into a powerful beam, increasing cloak by 15 and attack by 10
30 Missions Ended - 9th Tier
Combat Analyzer: a specialized battle intelligence, increasing attack by 15 and defense by 5
34 Missions Ended - 10th Tier
Chron-Transistor: increases both energy and shield charge rates by 5.
38 Missions Ended - 11th Tier
Mass Storage Pod: increases cargo capacity by 60
(It will be added to your inventory as an Artifact. Be Cautious as you can Scrap it.)
42 Missions Ended - 12th Tier
Subspace Compressor: Channels spacial folds into energy waves, boosting defense and energy by 15
46 Missions Ended - 13th Tier
Tachyon Router: Very efficient subsystem connector, boosting scan by 25 and energy by 10
50 Missions Ended - 14th Tier
Impact Absorber: Increases shield by 20 and hull integrity by 45
54 Missions Ended - 15th Tier
Omnibase Chassis: Planet Structure. Size:5, Mining: 3, Research: 3, Artifact: 3, Attack: 1000, Defense: 1000. Added to cargo as a Chassis.
58 Missions Ended - 16th Tier
Exotic Dynamo: Increases energy by 20 and attack by 15
62 Missions Ended - 17th Tier
Field Balancer: Increases shield by 20 and shield recharge rate by 10
66 Missions Ended - 18th Tier
Drone Cluster: Increases attack by 20 and hull integrity by 40
70 Missions Ended - 19th Tier
Dark Mutagen Battery: Increases energy by 20 and invasion attack bonus by 40.
74 Missions Ended - 20th Tier
Council Base: Planet Structure. Size: 2, Invasion Defence: 500, Population: 100, Limit: 1 per planet. Cost: 10,000,000 Credits and 15 Political Favor.
Note: The Council Base is not a single-use artifact like the Omnibase. It will be added to your planet build list as a new buildable structure. You can build as many of them as you want, as long as you have enough resources. (Note: one per planet)
78 Missions Ended - 21st Tier
Tractor Beam: Increases hull integrity by 50 and defence by 25
82 Missions Ended - 22nd Tier
Flux Ringdisc: An advanced prototype multi-transmitter. Increases scanning and cloaking abilities by 30.
86 Missions Ended - 23rd Tier
Krionite Transducer: A powerful transducer for krionite gas implosions. Increases energy charge rate by 8 and attack by 30.
90 Missions Ended - 24th Tier
Chron-Pulse Drive: Increases defense by 30 and max shield by 50.
This is currently as far as the mission completion rewards are known to go.
See also: Mission Artifacts, Missions, Mission Chains.