Charon Industries

"Charon Industries. Big umbrella company that got a hand in every major market you can think of. Even messed with cryogenics a few years back, but it looks like their largest profit comes from weapons and technology; they own most of the stuff on the ship."

- Epsilon describing Charon Industries

Charon Industries is a weapons, technological, and cryogenics corporation that has ties to the United Nations Space Command. Revealed to be a corrupt corporation, Charon Industries has a large involvement in the events of the series during later seasons.

Insurrection
The Insurrection, also referred to as the Resistance, is a military outfit specializing in cryogenics, with one member appearing in Recreation and the official faction in Season 9. The elite group serve as Charon Industries private security force. According to the Director of Project Freelancer, however, they are a military force made up of soldiers who have broken off from the UNSC. The faction serves as the secondary antagonists of the Project Freelancer Saga.

They had been at odds with Project Freelancer for a while, but mainly wanted revenge after a handful of agents raided and destroyed the Bjordinal Cryogenics Research Facility (Agents North and South Dakota infiltrated the facility with backup from Carolina, but unknown even to them, Agent Texas had planted a bomb that destroyed the facility, killing all but one soldier, the Demo Man). Later, when Project Freelancer stole the Sarcophagus from a Charon building, a large number of soldiers were killed by a MAC round fired by the Mother of Invention.

Later, C.T. betrayed Project Freelancer, revealing her ties to the Insurrection. The Director of Project Freelancer sent his agents on a mission to the Longshore Shipyards where C.T and the Insurrectionist Leader are holding Project Freelancer equipment. When nearly all the other Insurrection soldiers are either killed or defeated, C.T and the Leader are cornered by Tex and Carolina, and the battle that ensues results in C.T's death, and the Leader donning her helmet and identity as a form of remorse for her death.

Desert Dig Team
The Insurrectionist Leader, now posing as C.T, led a team of humans and aliens on an archaeological dig, killing the original members Tucker had been assigned to and attempting to breach the temple where Tucker was guarding an artifact. After the artifact is used to revive Epsilon, a battle ensues with the Leader and Tucker face to face on the roof of a nearby building. Though the Leader refused to reveal to Tucker who he was working for, it is highly likely he was doing this for Charon Industries. Epsilon met up with them and after being insulted by the Leader (being called a "thing"), Epsilon fired a laser at the Leader, killing him instantly.

Space Pirates
The Space Pirates were hired to clear the planet Chorus to allow Malcom Hargrove access to the planet without interference. They serve as the primary antagonists of the Chorus Trilogy, and are mainly led by Locus and Felix; though the latter was not revealed as a Space Pirate until much later.

In order to keep the Federal Army of Chorus and the New Republic at war long enough to kill each other off, the Space Pirates killed off their leaders, effectively driving further division between the two factions. Locus was assigned to the Federal Army while Felix was assigned to the New Republic. For years they kept the war going, until the Reds and Blues crashed onto Chorus. Felix finds them and recruits them into the New Republic, seeing them as good scapegoats to "lead" the rebels. Locus, on the other hand, captures a few of them when attacking Crash Site Bravo. Both parties see the Reds and Blues as heroes that can end the war, but when Malcom Hargrove, posing as Control, views them as a threat, he orders the Space Pirates to kill them. When Felix arrived to "help" the Reds and Blues, he reveals his true allegiance, also effectively revealing the true nature of the civil war. Before they can be killed, however, Carolina, who had been posing as a Space Pirate for some time, had rescued themand transported them away from the F.A.C Outpost.

Locus and Felix were ordered by Control to inform the two armies' leaders that the Reds and Blues had died, leading them to one final controntation to end the war. Meanwhile, the Space Pirates offered a deal to the Reds and Blues; in order to get them out of the way, they offer the Reds and Blues a free, one-way ride off of Chorus in return for not speaking a word about their involvement there. The Reds and Blues turn down the offer, however, and lead an ambush on the radio jammer where a number of them are stationed. While Washington battled Locus, Tucker and Epsilon baited Felix into bragging about their manipulation of the civil war, which was recorded on Tucker's helmet-cam and, after the radio jammer was destroyed, broadcasted to the capitol city where the two armies were fighting. Both leaders called for a ceasefire, effectively ruining the Space Pirates' plans. Locus and Felix teleport away, vowing they will return.

While most of the Space Pirates are captured, Locus and Felix report back to Control, who orders them to "go to war". Their conversation is interrupted by the Reds and Blues, who reveal Control's identity as Malcom Hargrove and state their intentions to fight back against Charon Industries. After the transmission, Malcom is revealed to be in possession of Agent Maine's helmet.