Prion variant was the deadly pathogen engineered by Jonas Hodges of the Starkwood company before Day 7. The development of the pathogen was ordered by a cabal of businessmen led by Alan Wilson who conspired to cripple the security of the US in order to gain defense contracts.
The prion variant was an altered form of the Creutzfeldt-Jakob disease, and attacked the brain and nervous system causing dementia, physical deterioration, and eventually death. Starkwood engineered it to be lethal within a shorter period (one or two days). The pathogen would still be active in the human body for two hours after death, and it could be destroyed by heat of at least 5,000 degrees fahrenheit. The original pathogen was native to the East Congo. An experimental treatment for the disease was theoretically possible using stem cells.
Before Day 7
Sometime before Redemption, a cabal of twelve American businessmen which included Alan Wilson and Jonas Hodges planned the development of a biological weapon. Their intention was to use it in the United States crippling the nation's security in order to gain defense contracts. The group trusted the development of the pathogen to Hodges through his company, Starkwood.
Hodges got in contact with Sangalan general Benjamin Juma and he agreed to provide Hodges with a safe place for him to develop the biological weapon, while Hodges would supply him with weaponry for another attempt at a coup. After the weapon was developed, Hodges and Juma began testing the prion variant infecting native Sangalans in remote areas. The villagers exposed exhibited mental degradation, uncontrollable movements, and other symptoms. As rumors spread of the terrorism, Juma fire-bombed the areas to destroy all the evidence.
Eventually, the pathogen was engineered to Hodges' satisfaction. In exchange for assistance with his political agenda and an invasion of the White House, Juma offered to ship the completed prion variant experiment to Washington D.C.
Arrival and transportation
Juma's men shipped the prion variant container from Pointe-Noire to the Port of Alexandria, where Hodges had sent a team of mercenaries led by Stokes to retrieve. Stokes had reached a deal with Port Authority supervisor, Carl Gadsen, to let them get their container out. Gadsen wasn't aware that the container had a bio-weapon because he was told they were smuggling electronics.
After Mitch verified the integrity of the bio-weapon, Stokes authorized the transport of the container. Stokes then ordered Carl Gadsen to be killed. However, Jack Bauer shot Cooper in order to save Gadsen, and subsequently started a shootout to prevent the bio-weapon from falling into Starkwood's hands. Jack managed to intercept the truck with the container and drove away from the port. While driving on Highway 236, he noticed something was wrong with the container and found a gash on the side caused during the shoot-out. He closed the opened valve to stop the dispersal, but became the first person infected with the prions in the USA.
After this, Stokes and his men intercepted Jack and retrieved the container again via helicopter, taking it to the Starkwood compound. Sunny Macer and CDC officials arrived at Highway 236 and established a perimeter to avoid further infections, but it was concluded that the dispersal was minimal.
CDC director Ben Landry briefed President Allison Taylor and the Joint Chiefs of Staff about the weapon. Also, Sunny Macer explained to Jack Bauer that a treatment for the infection was theoretically possible: an experimental treatment at Bryden University using stem cells from a compatible family member (in his case, daughter Kim Bauer) could save his life. But the likelihood of success was completely unknown and Jack ended up rejecting the treatment not wanting to bring his daughter into this.
Starkwood uses the prion variant
Upon its arrival at the compound, the lead Starkwood scientist Tom Chapman, verified the container and assured Hodges that the weapon would be ready in a few hours. Without Alan Wilson's consent, Hodges ordered Chapman to load the prion variant onto some Python missiles, and the rockets were loaded with RP-7 rocket fuel. While they were doing this, Tony managed to infiltrate the compound and gain a visual of the prion canisters for Jack to identify. This prompted President Taylor to authorize an airstrike on the compound. However, Hodges used the rockets to force her into aborting the airstrike and meeting with him to accept his demands.
At 1:25am, with indirect authorization from the President, Tony Almeida managed to rig the RP-7 fuel tanks using C4 charges, destroying them right when Chapman was about to launch the missiles. The extreme heat of the explosion wiped out the prion particles in the rockets. After the threat was averted, Hodges and Greg Seaton were arrested at the White House.
The missing canister
Unknown to most people, Tony had convinced a Starkwood operative, Robert Galvez, to smuggle a single canister of the prion variant out of Starkwood for him. Tony, who was working the entire time with Cara Bowden for the group led by Alan Wilson, had agreed to provide them with the bio-weapon. Tony helped Galvez escape through the FBI perimeter, but later killed him when he tried to blackmail him.
After meeting with Cara at a motel, Tony convinced her to take advantage of the chaos caused by Hodges' threat, and use the weapon immediately. Cara consulted with Alan Wilson and the group of conspirators via teleconference, but they were reluctant to do so, having an original plan to use it in six months from that point instead. Wilson, however, believed in Cara and convinced them to green-light an attack.
The plan was to use some Muslims living in the US and plant incriminating evidence on them to frame them for the attack. Tony and his men forced Jibraan Al-Zarian to serve as courier in the Washington Metro, while Cara took the canister to a scientist who would have it ready for detonation. After leaving Jibraan at the subway, Cara intercepted him and left the canister for him to carry. After Tony was captured, Jack contacted Jibraan and helped him walk out of the subway with the ticking canister. When Jack found him, he took the canister and threw it inside a CDC enclosed vehicle where it detonated safely.
After Tony escaped FBI custody with Jack Bauer as a hostage, he told Cara that the prion variant was still alive in Jack's body. Bauer was transported to a makeshift medical facility, where Cara's biochemist found that the toxin was more intact than previously thought, and that the toxin would live on after Jack's death for two hours. He also mentioned only extreme heat above 500°C would truly eliminate the biotoxin.
Before the biochemists could extract the prion variant from Jack, he broke free, killing his captors. He attempted to escape, but Tony caught up to him. Jack nearly incinerated himself and the remaining toxin with gasoline and a flare, but Tony stopped and captured him. Tony revealed to Jack that he had no intention of retrieving the toxin, and that he only participated in the prion variant attacks to get close to Alan Wilson, who was actually the man behind Charles Logan and responsible for the death of Tony's wife, Michelle.