― Agent Jones[src]
Jones assisted in the interrogation of Morpheus with his fellow Agents. When Neo and Trinity attempted to rescue Morpheus from the government building where Morpheus was held, Jones materialized in the body of a helicopter pilot named "Kim" who was desperately calling for backup. Jones used his extreme speed to dodge Neo's bullets, but failed to kill Neo, who was similarly able to avoid fatal wounds, although he did succeed in grazing him in the thigh, stunning him long enough for Jones to prepare to finish him off at point blank range. Trinity shot Jones through the head at close range, saving Neo but merely sending Jones out of the body he had possessed.
Jones survived most of the movie. He was last seen with Agent Brown, watching the fight between Neo and Agent Smith. After that, Jones was either deleted or upgraded to become Thompson, Jackson, or Johnson, but if he was upgraded, his method of speaking indicates that he was updated to become Johnson.
His statement towards Neo when he is prepared to kill Neo, "Only Human," implies that he has a degree of dislike towards humanity, although not to the extent of Agent Smith.
In The Matrix: Path of Neo, he fights Neo one more time in the part of the game called "Red Pill rescue", along with Agent Brown. Unlike the Upgraded Agents of the next level, he cannot regenerate his health. After the player has rescued all four Redpills, Jones is never seen again, same for Brown.
Sixty years after the end of the human-machine war, Agent Jones was present as one of the members of the Agent trio lead by the recreation of Agent Smith inside a modal written by Thomas Anderson (Neo's identity while being subdued inside the seventh version of the Matrix) alongside Agent White. Inside the modal, Jones served a similar role to his original self, chasing the modal's version of Trinity through the Lafayette onto the rooftop. However, unlike the original events, the Agents captured Trinity. Bugs spied on the fight, but was discovered by a surveying police chopper and came into contact with the Agents, who tried to kill her. On street level, White and Jones took possession of police officers, forcing Bugs to hide inside a key shop. Initially finding the key shop empty, the Agents soon encountered Smith, who had in the meantime accepted a redpill from Bugs and was showing visible aftereffects. White and Jones realized Smith had been compromised, leading them to chase Smith and Bugs through a derelict building, but the Agents were ultimately unable to prevent the two from escaping the modal.
Later, the modal was deleted, presumably by the Analyst. As a result, Jones was also deleted.