While the exact purpose of the pathogen is unknown, exposure to it has increased Chloe Armstrong's intellect and given her the ability to heal rapidly. She has an innate but unconscious understanding of the Nakai language, being able to recognize the meaning behind the symbols without actually understanding them. It also causes her to sleepwalk, during which time she seems compelled to study Destiny. It has also resulted in her growing hard alien skin in somewhat random patches, beginning with a patch that grew from the site of a bullet wound she suffered. (SGU: "Space", "Lost", "Incursion, Part 1", "Incursion, Part 2", "Intervention", "Pathogen", "Cloverdale", "Trial and Error", "Visitation")
The presence of the pathogen was first hinted at when Chloe Armstrong was somehow able to understand the pictographs within the computer system of a crashed Nakai fighter. Later, during an invasion by the Lucian Alliance, she was shot in the leg, only for the wound to heal at an unnatural rate. (SGU: "Space", "Lost", "Incursion, Part 1", "Incursion, Part 2", "Intervention")
Not long after, Chloe began sleepwalking, during which time she would study the ship and take notes. At this point, the Destiny expedition realized she had been compromised. Dr. Nicholas Rush suggested using the interface chair as a possible cure, but it failed to work. He worked out an agreement with her to keep her infection secret in exchange for her help in solving complex equations. (SGU: "Pathogen")
When Lt. Matthew Scott was infected by an alien creature, however, Chloe had to expose her secret in order to save him, as the pathogen had rendered her immune to the creature's infection. Scott was given a blood transfusion from Chloe, saving him by infecting him with the same pathogen. While stuck in a hallucination Scott is given a vision of what Chloe is becoming when he see's her face half transformed by the pathogen staring darkly at him.
Scott's system effectively managed to kill the pathogen, while Chloe continued to mutate, growing alien skin from the location of the bullet wound. It is unknown what caused Scott's resistance to the alien virus but it is possible that the virus was weaker in a tranfussion and his system was able to recognise and kill it. (SGU: "Cloverdale")
Her mutation continued to advance, resulting in alien skin growing near her elbow on her right arm. The alien influence over her mind also settled in, allowing her to control it to an extent. This allowed her to deduce how to plot a new FTL course for Destiny. (SGU: "Trial and Error", "Malice", "Visitation")
The pathogen has also seemed to increase her strength. When Eli Wallace turned to leave, she grabs his arm and Eli winces. When she says she can help, Eli decides to let her out but Cpl. Baras refuses to do so without Colonel Everett Young's permission. Frustrated and impaitent, Chloe slams Baras' head into the bulkhead twice until he falls unconscious. It is later revealed that she broke the guard's arm. (SGU: "Resurgence", "Deliverance")
After using the pathogen to summon the Nakai to help with the drone attack on Destiny, the pathogen is removed by the aliens onboard one of their motherships and Chloe is returned cured to Destiny. Chloe retains some of the knowledge she gained and is able to still do complex equations, but is sure that whatever the aliens got when they removed the pathogen will only make them more determined to capture Destiny. (SGU: "Resurgence", "Deliverance")