The Faction was a group of villains whose goal was to get Ben Tennyson's Omnitrix and use it to humiliate and kill Azmuth, serving as the main antagonistic force of the first two arcs of Omniverse. With Malware killed by Ben, the Faction no longer has any purpose and was disbanded.
After Malware obtained a crude, corrupted, and incomplete blueprint of the Original Omnitrix, Dr. Psychobos used the blueprint to create a device called the Nemetrix. The device only needed predator DNA to be complete.
With this in mind, Dr. Psychobos hired Khyber, the so-called "The Greatest Huntsman in the Galaxy," to obtain DNA of the most dangerous predators in the galaxy. After acquiring the required DNA in many hunts, the Faction captured and used a former Plumber, Phil Billings as a test subject.
The test was proven a failure after Phil - a high functioning being - entered a catatonic-like state on account of not being able to control the feral nature of the Nemetrix. Phil's replacement was an Anubian Baskurr, later named Zed, that could more successfully handle the bestiality inherent in the Nemetrix's transformations.
The Faction subsequently launched a series of attacks on Ben, planning to use the Omnitrix to achieve their goals. After Dr. Psychobos managed to steal a regulator from the Omnitrix, however, the group began to focus more solely on Azmuth. They had not yet finished their business with Ben, though, as another attack was made on Ben as a distraction so as to allow Malware to obtain Galvan security codes from Rook's truck that would allow them to infiltrate Galvan Prime.
On Galvan Mark II, the Faction cornered Azmuth but quickly lost their unity after Azmuth summoned Ben. Khyber desired to complete his hunt for Ben, Dr. Psychobos wanted to humiliate and kill Azmuth, and Malware had plans for the planet itself.
After their disbanding, Dr. Psychobos was defeated by a joint effort between Ben, Rook and Azmuth. Khyber abandoned his pet and fled, while Malware initiated his strike on Galvan Prime, but was subsequently defeated. Dr. Psychobos was arrested by Galvan forces, while Khyber's former dog, eventually named Zed, was adopted by Kevin. Malware was killed in his defeat by Feedback, but Khyber remained at large until Stuck on You.