Chief Red leads the Arkz against the Pioneer2 government to destroy the dangerous CARD technology. You recieve all of your main mission assignments from Red. His goal is to find the "Great Shadow" and destroy it.
Red had two daughters, whom he loved very much. But somehow, they died. Because he loved his daughters so much, he wished to be with them again. When the government offered to clone them back into existance, he agreed. The government soon prepared two wonderful little clone girls of his deceased daughters. The problems arose when they went further. Without Red or his daughters' permission, they continued makeing more little girls. The government and Dol Grisen were working on a "Clone Weapon" project, which involved horribly mutating humans in order to enhance their powers. Many of the clones were not stable, and probably insane or evil. When the un-altered clones of Reds' daughters saw what they had been used to make, they held hands and killed themselves in a double suicide pact. Devastated, Red fled from P2, and became the leader of ARKZ, to oppose such great wrongs.

It is suspected that this NPC may be related to, or somehow BE Principal Tyrell from the first PSO game. However, if it was, he'd have to be on extensive Newman Growth Control Drugs, which seems unlikely, as he's not sick at all from any side effects. The character of Red is much younger, shorter and slimmer then Tyrell. His name is Red, and Rico went by the name "Red Ring Rico" who was associated with red objects. And after losing Rico, he had ANOTHER two daughters? With who? Why?

Chief Red's Officer
AKA:
A Human Male
Relations:
Occupation: Serves as a secretary/aide to Chief Red
Special Powers:
Affiliations: Arkz
Enemies:

Curiously, this NPC is never named. He serves the same function as Karen from the Hunters' CARD lab. Because the entire Arkz R-Base is a lot less formal and strictly run then P2, he comes across as more personable and friendly. This guy is good at heart, just like Karen, and serves to explain certain things to a greater degree, and sometimes provides a personal angle to situations.

Chief Pentaglass
AKA:
A Human Male
Relations:
Occupation: Commander of the Morgue
Special Powers:
Affiliations:
Enemies: The Arkz

Chief Pentaglass is the leader of the Hunters Side Story characters. He issues all the official orders, and sends you on most of your missions. Pentaglass is not a very involving character. He has the simple motivation of being promoted to a higher rank, and getting more power for himself. He always wants to look good in the eyes of his superiors, and likes the thought of controlling others. Pentaglass is meant to be a characterization of the pompous authority figure. He tries to act tough and gruff, but sometimes ends up coming across as silly and funny, even if it isn't his intention.

Karen
AKA:
A Human Female
Relations:
Occupation: Secretary of Chief Pentaglass
Special Powers:
Affiliations:
Enemies: The Arkz

Karen is the level-headed counterpart to Pentaglass. She helps fill in the details about his orders, and often provides a personal angle on the circumstances and consequences of your missions. She is polite and pleasent, with seemingly no great aspirations to higher powers. She ultimatly wants what's best for everyone, and seems quite good at heart.

Dol Grisen
AKA:
A Human Male
Relations:
Occupation: Leader of the Pioneer 2 Government
Special Powers:
Affiliations:
Enemies: The Arkz

This officer is a major source of problems for the people of P2. He ousted Tyrell, and demoted him to Environmental Studies position, after he couldn't explain the events of Fallz and Olga. Dol is very interested in clone technology, thinking it will give him a huge military advantage and a limitless supply of controlable soldiers. Through his research efforts, the CARD technology is also discovered. He later breaks relations with Coral, and nearly starts a war/rebellion against the home world. Fortunatly, this error is resolved, and war does not result. Dol Grisen then turns his attention back to his infamous Clone Army. He realizes there will need to be space and resources available for his new army, so he has the military kill off hundreds of androids to free up what he requires. This terrible massacre is called the OPSS incident. The current military was used to kill the innocent androids. Once Dol and his scientists discover The Germ, he abandons his Clone Army project, in favor of CARD. Not having learned anything at all from the covered-up Olga Flow incident, he dumps all the failed clones in an abandoned lab. (probably being unable to kill them, much like the corrupted Flowen)

Castor And Pollux
AKA:
Twin cloned human females, light tan skin, face markings, one with red hair, the other blue
Relations: Father- Chief Red
Occupation: Military experimental weapons
Special Powers: Blade for arm, Gun for arm
Affiliations:
Enemies:

Commander Red's twin daughters. They were presumably killed in some kind of horrible accident, which devastated Red. Red heard about Dol Grisens' cloning project, and decided to have his daughters copied, to bring them back to be with him. However, Dol Grisen made multiple copies of the children and kept some of the copies for himself, and twisted them into horrible weapons. When the first clones of Red's daughters saw what they were being used to create, they held hands and killed themselves to stop Dol Grisen's scientists. Their double deaths lead Red to begin his uprising against the Hunters, Grisen, and the P2 government. Red later goes to see what happened to his daughters' clones in the abandoned lab where Dol Grisen dumped all the failures. He finds a horror there.
Castor is the blue twin. She has a huge gun biologically affixed to her right arm. Her hair forms two rounded tentacles, which she can move at will. The gun is too heavy for her small form, so she walks around half-bent over. She stands much like an ape, wobbling on her legs and weaving about with the weight of the weapon. She must kneel to fire it. This clone is imperfect. She has a gash in her side where her green blood boils away into the air in a shower of sparkles. She loses her HP with a yelp as she drains away.
Pollux is the red twin. She has a huge sword biologically grown from her right arm. Her hair forms two flat spiky tentacles, which she can move at will. Her sword is not so heavy that it pulls her down, so she walks upright. It is twice as long as she is tall, and has a red bio-photon blade. This clone is imperfect. She has red glowing guts that hang out of her stomach area and convulse. She does not lose her HP.

Blitz
AKA: It's not his real name
A Human Male
Relations: Two children: Kylria and Kranz. Also, a deceased wife
Occupation: Ex-Hunter, researcher
Special Powers: Survived being infected by The Germ
Affiliations:
Enemies:

Blitz the RAmar is the mysterious father of Kylria and Kranz. He was one of the hunters aboard the P2. Because he took so many missions, and stayed away down on Ragol for so long, it lead his wife to divorce him. She took with her their daughter Kylria, and raised her harshly until she died some years later. Once his wife died, Blitz re-appeared in Kylria's life to become her trainer and mentor. He didn't reveal to her that he is her father. Later on, he resigned from being an official Hunter, and took off to explore Ragol on his own. It was while on one of these missions that he discovered The Great Shadow. He knew it was evil, so he tried to fight it. He didn't win, but he was able to escape with his life. He naturally returned to P2 for help...but unwittingly took "The Germ" back with him. Anyone he encountered (mostly lab workers) died from an infection of The Germ. However...because Blitz himself lived, people were able to isolate and study the Germ.

Susan
AKA:
A Newman Female
Relations:
Occupation:
Special Powers:
Affiliations: Is like an older sister to Creinu, Raised Peko
Enemies:

Susan is the closest thing to family that Peko, the Arkz FOnewm knows. Because newmen don't come from families, most of the time, Peko doesn't know what it's like to have a real mother. Susan helped raise peko, and still keeps him in line to this day. (yells at him if he does something wrong, etc.) She is like an older sister to Creinu, the Arkz FOmarl. She is known to take anti-aging drugs.

Could this NPC that you never see in the game be Sue from Black Paper?

Sofia
AKA:
A Newman Female, Brown Skin, long white hair
Relations: Sister-Sil'fer
Occupation:
Special Powers:
Affiliations: Is in love with Break
Enemies:

Sofia is a casualty of suspicion and the Germ. One day, being suspicious of Break, with whom Sofia was having a relationship, Sil'fer followed them. They were going to the area of the Great Shadow, a place especially infected with The Germ. Break and Sofia had brought the antidote for themselves. However, they had not been expecting Sil'fer to follow them. The three were infected, and for some reason, Break had to use Sofia's antidote on Sil'fer. Sofia died on the spot, due to her infection. Sil'fers suspicion ruined Break's life, and killed her sister. Sofia had expressed that she never wanted to be cloned if she were to die. Somehow, she ended up dieing twice. The cause of her first death (that resulted in the clone you see killed by the Germ) is unknown. When she died for the second time, her body turned to dust, and so could not be cloned again. Sofia seemed to be a kind person and she is visible only in cutscenes.