Penumbra

Penumbra is a covert operations organization which operates throughout the AFS area. At times, the objectives of Penumbra seem to be at odds with the objectives of the AFS high command. Penumbra has also demonstrated a willingness to use tactics that are considered highly questionable by AFS high command. The current ranks of the Penumbra seem to be made out of different Earth based intelligence agencies such as the CIA, FBI, KGB, MI6, etc. (Penumbra Administrator Earhardt of Section 4 is from the CIA, at Langley.)
The Penumbra headquarters is in Tantalus Base on Abyss, Arieki. Players will have the opportunity to join Penumbra by running various missions for the director when they reach Abyss. However, you can also be a double agent working for the AFS by talking to General Perry at the south end of Tantalus Base. Whether or not you follow General Perry’s or The Director’s orders determines whether you get the Abyss Double Agent title or the Abyss Conspirator title respectively.
In order to even enter the Penumbra questline (i.e. have level one clearance), you should have taken Clean Slate from Corporal Wainwright, started the questline from Agent Perdu and completed Mind Bender, The Results Are In and Mind Slayer. Agent Perdu will give you level one clearance. By the time you get to Torden Abyss, you will be able to take Belly of the Beast from The Director to start the questline.
The Penumbra chain of command is divided into five independent cells, with each cell with higher clearance than the last.
=== Section 1, Information Technology ===
The first cell, Section 1, deals with Information Technology. This is of course only a facade; their actual function is counterintelligence by means of monitoring all communications, stored information and databases within AFS. They are able to do this via the "Diogenes Directive" which supposedly amended Article 268 of the AFS Uniform Code of Military Justice which deals with the privacy of any and all soldiers of the AFS. The current head of Section 1 is Penumbra Administrator Alexander. In order to advance to level two clearance and Section 2, you will need to complete The Human Factor.
=== Section 2, Covert Surveillance ===
Section 2 deals with Covert Surveillance, which does exactly what it stands for. Unlike Section 1, however, Section 2 takes a more active role in reconnaissance of both internal and external assets. (Though there has been no known example of the latter.) They also help Section 1 in terms of counterintelligence. The current head of Section 2 is Penumbra Administrator Pearce. In order to advance to level three clearance and Section 3, you will need to complete Enemy of the State.
=== Section 3, Espionage ===
Section 3 deals with Espionage, and it's primary function is to gather intelligence from non-human factions such as the Thrax, Brann, Eloh, Neph and the Foreans. Their secondary function seems to be the acquisition of exotic weaponry, armor, logos elements. Specifically they seem to be quite interested in Bane weaponry be it conventional, biological or otherwise. Section 3 apparently has bunks for their field agents, as well as supplies and amenities presumably to have entire covert cells ready for black ops. The current head of Section 3 is unknown, but your primary contact is Penumbra Agent Crawford. In order to advance to level four clearance and Section 4, you will need to complete The Goggles That Do Nothing and be a minimum of level 43.
=== Section 4, Special Weapons Technology ===
Section 4 deals with Special Weapons Technology. Here, recovered exotic weaponry, armor and equipment from alien races by Section 3 are processed and presumably reverse-engineered by Penumbra researchers and personnel. Their primary function seems to be that of salvage and analysis as opposed to a dedicated research facility. Most of the equipment are being analyzed by machines that seem to project logos similar to the Away From Keyboard logos onto the subject matter. Listed below are what they have recovered:
1) An intact Bane Juggernaut
2) A Bane laser or drill(?)
3) & 4) Two Brann aircraft/hovercraft
5) Disassembled parts of a Bane tesla coil
6) A Bane Stalker head
7) & 8) Two Thrax pistols
9) & 10) Two Thrax rifles
11) A Thrax Technician EMP pistol
12) A Forean bow
13) A Forean rifle
(in the enclosed room)
14) A Brann turret
15) A Bane mortar
16) A jury-rigged Thrax Technician ballistic turret
17) A Bane light
18) Unidentified #1, possibly a weapon
19) Unidentified #2, quadruped object/module
There is a storage room filled with what seems to be scrap items:
1) Remains of a Bane tesla coil
2) A broken Bane control chair
3) An intact Bane light
4) A destroyed Bane command table
Current projects of Section 4 entail; 1) research into creating a Human or Brann linker, via use of modified brainstems which will be implanted into subject Humans or Brann, 2) development of an autonomous AFS mech, similar to the Bane Juggernauts and 3) research into Amoeboids, the pathogens within their body and the pseudopods they use to launch them.
The current head of Section 4 is Penumbra Administrator Earhardt. In order to advance to level five clearance and Section 5, you will need to complete Hyper Links, Giants of the Abyss and Pathogen
=== Section 5, Special Projects and Omega Labs ===
Last but definitely not the least is Section 5, dedicated to the development of exotic weaponry for the Penumbra and for the AFS. Unlike Section 4, which primarily deals with salvage and analysis, Section 5 takes the initiative in weapons development projects. It is here that the Thraxus Machina was developed with the aid of captured and reversed-engineered Thrax gene pods possibly from a Bane barracks. However, Section 5 is currently under code Red as the Special Projects division is overrun by berserk Thraxus Machina (led by the Thraxus Machina Supersoldier and the Omega Labs is overrun by “Believer” Brann, Machina and Humans. 
You will have been referred to Penumbra Researcher Ackroyd by Penumbra Administrator Earhardt to exercise damage control in Section 5. You will notice that Penumbra Researcher Chambers also has a couple of missions for you in Section 5; Complete Product Recall, Prototype, Chambers of Horror and The Penumbra Strain then talk to The Director. You will be able to get The Abyss Looks Into You, at which point you can deliver the falsified report to and either tell him the truth to earn the Abyss Double Agent title or lie to him and earn the Abyss Conspirator title.
The head of Section 5 was Dr. Mathias Sandorf, however there are certain circumstances that have put into question his leadership. Your main contact(s) will be Penumbra Researcher Ackroyd and Penumbra Researcher Chambers in the external Special Projects area and Special Agent Rudoy and Special Agent Garrett in the Omega Labs.
See: Section 5: Omega Labs 
=== List of Known Named Penumbra Agents ===
Foreas Valverde Plateau
Agent Perdu
Arieki Torden Abyss
The Director
Penumbra Administrator Alexander
Penumbra Administrator Pearce
Penumbra Administrator Earhardt
Dr. Mathias Sandorf (Renegade, Believers)
Penumbra Researcher Ackroyd
Penumbra Researcher Jacobs
Penumbra Researcher Chambers
Penumbra Researcher Vancamp
Penumbra Researcher Stroud
Penumbra Researcher Davies (Deceased)
Penumbra Researcher Foley (Deceased)
Penumbra Researcher Markham (Deceased)
Penumbra Operative Spence
Penumbra Operative Wilkins
Special Agent Rudoy
Special Agent Garrett
Penumbra Agent Crawford
Penumbra Agent Boddiker
Penumbra Agent Coombs
Penumbra Agent Hayden
Penumbra Agent Trent (Deceased)
Agent Maxwell
Field Medic Jackman
Crafting Supplier Hobart
Medical Crafting Supplier Branson
Armor Supplier Manchasa
Armor Supplier Pantoliano
Armor Supplier Clemens
Armor Supplier Brooks
Weapons Supplier Van Dyke
Weapons Supplier Martin
Weapons Supplier Lane
Weapons Supplier Drake
Foreas Valverde Howling Maw
Field Commander Welling
Unknown
General Creelig (mentioned by Field Commander Welling)
=== Notes ===
*”…We’re everywhere, trust me” ~ Field Commander Welling
*There is a Penumbra outpost manned by a cell somewhere in Howling Maw led by a boss Penumbra Captain. It is uncertain whether or not the developers had intended to give them a purpose or a mission marker or if they’re just fluff.