Collaboration with the First Sons
When DARPA collaborated with the First Sons by funding the Ray Sphere, Moya Jones worked directly with Kessler and as an alliance between DARPA and the First Sons, during the Ray Sphere development.
Moya had Kessler show her one of the tests subjects, David Warner, and explain Ray Sphere's effect on him after each time he was exposed to it, though she is disgusted by Kessler's tests. Though Moya and DARPA were unaware of Kessler's true intentions for the Ray Sphere, he used the Ray Sphere to create the Blast. Subsequently, Moya and several soldiers attempted to arrest Kessler for causing the Blast. However, Kessler killed the soldiers and told Moya that the Ray Sphere was with NSA agent John White. Moya then made it her main focus to obtain the Ray Sphere for DARPA by finding John.
Working with Cole
After the Quarantine was put in place following the Blast, Moya worked to track down John White. After Cole MacGrath attempted to break through Quaratine, he ended up trapped in a decontamination unit and the door shuts. Being a powerful Conduit, Moya saw him as an opportunity to get the Ray Sphere. Moya revealed herself to Cole, and lied that John White was her husband, and lost contact with him after the Blast despite her connections.
Moya shortly made an agreement with Cole: if he can find the Ray Sphere and John, she will clear Cole's name and free him from the Quarantine. She then taps Cole's phone and has him return to Empire City. Moya has Cole carry out various missions, such as collecting John's Dead Drops, tracking down her contacts like Brandon Carey, twarting many of the Reaper and Dust Men's operations.
Attack on Empire City
As the attack on Empire City continued, Moya prepared to lead a military operation to capture Cole, feeling that he is too powerful to remain a free man. However, feeling Sasha would be a threat to the operation because of her love for Cole, Moya had Sasha found and later imprisoned, where her black tar is extracted hoping to use it against Cole. Subsequently Moya's troops invaded Empire City. Moya called Cole on his phone and told him how serious she was about the operation. Subsequently, Moya sent several soldiers to save Cole from David Warner, who tried to kill Cole believing him to be Kessler in disguise.
Eventually, Cole and David fought in a building where Moya called Cole on a phone and warned him to escape before the building is bombed by the military to kill David. Later at Steel Harbor, Moya told the military general that without Cole, DARPA and the military cannot replicate the Ray Sphere effect. Moya then suggested they move Cole far away from Empire City as David was still trying to kill him. As their attempts to capture Cole failed, Moya claimed they should change their methods to capture him. Shortly thereafter Moya and the military were able to track down Cole. Utilizing Sasha's tar, Moya was able to have Cole captured.
At Steel Harbor on a military ship, Moya tried to convince Cole to work for the military. However, he refused and Moya decided that a device should be implemented into his skull allowing them to have total control over Cole. However, Cole soon escaped with Sasha's aid after she broke from her cell. Moya, however, was able to stealthily attack Sasha from behind with a pipe. Sasha retaliates, though Moya is aided by several troops.
As the ship they were on began to sink because of a fight outside with Cole and David and military Conduits, the military general threatened to shut down Moya's operation because of her recent actions. Moya then killed the general with a gun and ran to see the carnage outside. As Cole kills David, Moya warned him that in one phone call, there could be a bounty on him. However, as ship sunk, Moya was suddenly trapped. Though Cole tried to save her, Moya told him to leave before he is killed by the water. With this, Moya died drowing in the ship.