
The basic faction system functions as a wheel. Each faction has two allied factions (next to them on the wheel), one archenemy faction (opposite them on the wheel), and two enemy factions (next to the archenemy on the wheel.
When you complete a mission that is a significant help to your faction, you gain reputation points with your faction. You also gain half as many points with your allied factions. However, you lose twice that much from your rating with your archenemy, and you lose an amount equal to your gain from your enemy factions. Thus, there is no way to manage a long-term balancing act by helping everyone equally; in the end, they'll all hate you for being a waffling turncoat.
However, these alliances do allow you to change your faction by working your way around the wheel. In the earlier stages of the game, switching factions is not hard, but the longer you are part of a faction, the harder it gets to change.
As you gain standing with a faction, new missions, merchants, and restricted knowledge become available. You can earn ranks and join in the capture of conflict towns.
It is worth noting though, that faction choices do not need to be made until Sector 2, which starts around level 15. Before then, there are no faction based missions that affect repuation standings.

Starting towns help setup a character for the style they wish to play. They provide weapons, starter schematics and plans for crafting, basic ammunition and some starting currency, whilst also acclimitising you to the larger game world.
These nine starter towns are separated into three categories, which define the type of quests available, and the types of quest rewards offered:
Combat (Kill style quests, weapons & ammo rewards)
- Boneclaw (Melee) - CHOTO based.
- Depot 66 (Pistol/Melee) - Traveller based.
- Zanesville (Pistol/Rifle) - Enforcer based.
- Terance (Pistol/Rifle)
- Mumford (Pistol)
Support (Mixed quests & rewards aimed at suppor skills)
- Clinton Farm (Melee/Rifle)
- North Burb (Melee) - Lightbearer based.
Crafting (Crafting styled quests, recipe book rewards)
- Midway (Pistol/Rifle)
- South Burb (Rifle) - Vista based.
All of the towns in Sector 1, including the starter towns, have no effect on faction status; this doesn't start until sector 2. You can do any/all of the quests available without affecting your standing with any of the 6 major factions.
Indeed, if you are planning to max out your AP, then you will need to perform the AP quests available in each of the towns shown on the map.
If you reach 165 in a skill, it is possible to receive a 'skill mastery' item. This is a storage item with extra stats, and each skill has its own item available. These items are not 'game breaking' or 'essential to have'; they are bonus items rewarded to those people that devote training to particular skills, so nothing to base characters around.
To receive the items, you must go and visit the relevant NPC listed below in Trader's Flat.
Note: This list is not complete as there may be more mastery rewards unfound or undocumented. If you know of more that should be listed here, please send them to me and I'll add them in.
Melee Skill Mastery
Warrior Frick, outside the melee merchant in Trader's Flat
Requirements: 165 Melee
Reward: Battered Shinai, Storage item with +8 Melee and +8 Melee defense
This training sword reminds you of how far you've come along the path of melee combat.
Dodge Mastery
Darien Swift, next to the melee trainer in Trader's Flat
Requirements: 165 Dodge
Reward: Pristine Cuban Cigar, Storage item with +358 Ballistic resists and +12 Dodge
As long as this cigar remains unsmoked, so shall you.
Pistol Mastery
Ping Oonishi, near the ballistics merchant in Trader's Flat
Requirements: 165 Pistol
Reward: Shiny Revolver Chamber, Storage item with +9 Pistol and +3 Stamina regeneration
Rifle Mastery
Honey Remington, near the ballistics merchant in Trader's Flat
Requirements: 165 Rifle
Reward: Slayer Bolt, Storage item with +10 Rifle and +5 Reflexes
This Crossbow Bolt is rumored to have killed over one thousand raiders without shattering.
Athletics Mastery
Tiger Bowens, in the courtyard next to the lightbearer sage's temple in Trader's Flat
Requirements: 165 Athletics
Reward: Tattered Running Shoes, Storage item with +50 Stamina, +5 Body, +5 Reflexes
Slowpoke's lucky running shoes; not much good for wearing anymore, but said to bring fortitude to their owner.
First Aid Mastery
Madonna Sykes, in the Vista camp in Trader's Flat
Requirements: 165 First Aid
Reward: Pristine First Aid Kit, Storage item with +4 Health regen and +4 Stamina Regen
Armor Use Mastery
Terullian Hammer, in the armorcraft workshop in Trader's Flat
Requirements: 165 Armor Use
Reward: Brass Nut Ring, Storage item with +260 to Slashing, Piercing, Crushing, Ballistic resists
Group Tactics Mastery (unconfirmed)
Trojan Blankenship, next to the armorcraft workshop in Trader's Flat
Requirements: 165 Group Tactics
Reward: Unknown
Social Mastery (unconfirmed)
Alvin Haggler, in the cooking workshop in Trader's Flat
Requirements: 165 Social
Reward: Unknown
Once you reach a certain faction level, and attain certain levels skills and/or mutations, it is possible to receive a 'capstone' reward. This is an extra ability rewarded for following the 'true callings' of the faction. These are not 'essential' or 'game breaking' abilities, just bonus abilities for those who decide to follow these faction-based builds.
To train these abilities, you should go and visit the relevant NPC listed below.
Note: This list is not complete as there are more capstone rewards unfound or undocumented. If you know of more that should be listed here, please send them to me and I'll add them in.
Banker's Hole (Traveller)
Baron Silias Marock, at the diner in Banker's Hole
Requirements: 80000 Traveler faction, 164 Melee, 164 Athletics
Reward: Scoundrel's Strike ability
This Melee ability (Traveler Capstone ability) inflicts 100 piercing damage to the target and stuns them for five seconds. The ability costs 81 stamina and has a two minute reuse time.
Morrigan, camp south of Banker's Hole -OR- Nick Bryer, at the front door of the main office in Banker's Hole -OR- Fred Bryer, by the mutagenics workshop in Banker's Hole
Requirements: 80000 Traveller faction, 164 Athletics, 164 Pistol
Reward: On Wires
On Wires increases your movement speed and boosts your ability to dodge attacks
Mike Stanley,west outskirts of Banker's Hole -OR- Martin Peralta, near the Social Trainer in Banker's Hole -OR- Edward Boswell, by the tent with Injured Travelers in Banker's Hole -OR- Louzsa Hearn, on the deck of the main office in Banker's Hole -OR- Ramon Scalfi, by the auction house in Banker's Hole
Requirements: 80000 Traveller faction, 164 Telepathy, 164 Sonic Influence?
Reward: Skullcrusher
Skullcrusher inflicts psionic and sonic damage to your foe.
Black Hill (Enforcer)
Major Thaddeus Mercer, middle building in main courtyard in Black Hill -OR- Private Martin Carvel, Black Hill
Requirements: 80000 Enforcer faction, 164 Armor Use, 164 Suppression
Reward: Juggernaut ability
This Armor Use Ability (Enforcer Capstone Ability) increases all physical armor values by 650 and increases all saves by 15% for two minutes. The power costs 81 gamma and has a five minute reuse time.
Note: This does not stack with Organize.
Private Timothy Carroll, near the CHOTA occupied farm SE of Black Hill
Requirements: 80000 Enforcer faction, 164 Dodge, 164 Rifle
Reward: Fatal Setup ability
This Rifle ability (Enforcer Capstone Ability) decreases your target's dodge rating by 120 for 10 seconds. It costs 81 stamina to use this power, and it has a two minute reuse time.
Note: This appears to have a 50m range, and is targeted like an attack mutation.
Lieutenant Carson, Black Hill -OR- Corporal Raven Skylark, Black Hill
Requirements: 80000 Enforcer faction, 164 Group Tactics, ? (likely 164 First Aid or Pistol)
Reward: Unknown
Chemtown (Tech)
Shae Davidson, in the Mutagenics workshop in Chemtown
Requirements: 80000 Tech faction, 164 Nano-manipulation, 164 Science
Reward: Tune Up Kit Knowledge and Tune Up mutation
Adds an extra crafting tab "Na" with the recipe to make Tune Up Kit (probably bugged and should be under Science).
Also adds an extra mutation under Nano-manipulation called Tune Up
This Nano-manipulation mutation (Tech capstone ability) increases a targeted vehicle's fuel efficiency by 25% and its Armor Use and Dodge ratings by 25 for one hour.
Ralph Keegan, in the forge next to the medical workshop in Chemtown -OR- Carlos the Brave, in the RV Park in the NW side of Chemtown -OR- Botty-June Harker, in the factory next to the weaponry workshop in Chemtown
(All three NPC's probably award same knowledge)
Requirements: 80000 Tech faction, 164 Thermal, 164 Ballistics
Reward: Short Fuse mutation
This Thermal Control mutation (Tech capstone ability) detonates volatile molecules inside a target causing 200 fire damage to the target and all others within 5 meters and stunning them for 3 seconds. This power costs 95 gamma and has a five minute reuse time.
Gaia (Vista)
Ranger Molly Frost, inside the West building of Shangri La, the geothermal powerplant downhill from Gaia -OR- Ranger Nate Anderson, on the deck of Ranger Hall in Gaia
Requirements: 80000 Vista faction, 164 Dodge, 164 Primal
Reward: Spider's Fang mutation
(both NPC's give the same knowledge)
This Primal mutation (Vista capstone ability) punctures the target for 135 piercing damage and inflicts 20 poison damage per second for 15 seconds. It costs 47 stamina and 47 gamma to use, and has a two minute reuse time.
Alyssa Keller, inside Science Workshop in Gaia
Requirements: 80000 Vista faction, 164 Rifle, 164 Sonic Manipulation
Reward: Thundershot mutation
This Sonic mutation (Vista Capstone ability) charges your next rifle shot with sonic energy that explodes outwards from the target and stuns all victims within 5 meters for 4 seconds. This power costs 47 stamina and 47 gamma and has a three minute reuse time.
Brother Trey Hurt, inside Medical Workshop in Gaia
Requirements: 80000 Vista faction, 164 Athletics, (probably also needs 164 Medicine or Nature)
Reward: Horse with No Name ability and Vista Stablemaster's Kit recipe.
Vista Stablemaster's kit appears under the heading "Horse with No Name" in the Nature crafting tab.
Horse with No Name ability appears under Athletics heading
This Athletics ability (Vista capstone ability) increases a targeted horse's fuel efficiency by 25% and its Armor Use and Dodge ratings by 25 for one hour. The ability costs 47 stamina and 47 gamma, and has no significant reuse time.
St. Sebastian (Lightbearer)
Mika Flint, by the Armor Merchant in the southern part of St. Sebastian's
Requirements: 80000 Lightbearer faction, ?
Reward: Unknown
Unknown
Location: Unknown
Requirements: Unknown (likely 164 melee, 164 Telekinesis)
Reward: Storm of Steel mutation
This Lightbearer Capstone ability inflicts 135 slashing damage and deals 15 slashing damage per second for 15 seconds. The ability costs 81 gamma to use and has a two minute reuse time.
Note: Used by Lightbearer Walter Curlew against players in the Banker's hole Traveler Capstone introduction mission
Warhall (CHOTA)
Destroyer Savral, Fire Station at end of runway by Athletics trainer in Warhall
Requirements: 80000 CHOTA faction, 164 Melee, 164 Patho-Transmission
Reward: Vile Strike mutation
This Patho-Transmission mutation (CHOTA Capstone ability) inflicts 175 crushing damage and infects a target with a disease that deals 24 disease damage per second for 10 seconds. This power costs 47 stamina and 47 gamma, and has a 1 minute reuse time.
Ravager Firedrinker, Blue-Skull's tent at mutagenics workshop in Warhall
Requirements: 80000 CHOTA faction, 164 Thermal Control, 164 Armor Use
Reward: Armor Melting
This Thermal Control mutation (CHOTA Capstone power) disintegrates the target's armor, removing 1000 points of piercing, slashing, crushing, and ballistic resistance for 30 seconds. The power costs 81 gamma and has a 30 second reuse time.
Marauder Wolftail, Blue-Skull's tent at mutagenics workshop in Warhall
Requirements: 80000 CHOTA faction, 164 Primal, 164 Mutagenics
Reward: Feral Mind mutation
This CHOTA Capstone ability grants the user 1000 psionic armor and 30% bonus to Body, Mind, and Reflex saves for 5 minutes. The power costs 81 gamma and has a 10 minute reuse time.
Note: this does not stack with Organize