Agent Jones

Agent Jones is a Matrix Agent and one of the two sidekicks Agent Smith along with Agent Brown. Originally created by The Architect to help put an end to the escalating Zion Resistance. Jones along with Brown found themselves serving as Agent Smith's sidekicks in a mission to obtain the access codes to the Zion Mainframe by capturing Morpheus so the Machines can destroy Zion with the access codes.

Discovery of an Informant
Jones along with Brown participated in an operativion led by Agent Smith, to capture Trinity so that se can be used to lure in Morpheus. The operation failed, but the Agents confirmed the the informant Cypher is real and Morpheus' next target is Neo.

Capture of Neo
Jones and Brown participated in a raid of a software company led by Agent Smith in order to capture Neo. The operation was a success they brought Neo into a cell for interrogation. Jones and Brown both believed that they were wasting time interrogating Neo, but Smith though Neo could be used to help them capture Morpheus. When Neo refused to cooperate, Jones and Brown restrained him while Smith placed a tracker in Neo, so that when Neo meets with Morpheus the tracker will inform them of their location.

Capture of Morpheus
After Smith's successful deal with Cypher, Morpheus was captured by Smith. While Smith interrogated Morpheus, Brown injected truth serum into his neck and Jones kept watch. A while later the three agents were discussing Cypher's death and how he failed to do his job. After Smith called them out of the room to interrogate Morpheus privately, the two return to inform him of Neo and Trinity's attack on their facility, but were surprised to see his earpiece removed. After the sprinklers activated due to the explosion caused by Neo and Trinity, Smith ordered Jones and Brown to find them and destroy them. Jones then possessed a helicopter SWAT pilot and approached Neo, so Neo emptied the bullets in his guns to shot at him but Jones used his superhuman agility to dodge all of those bullets. When Jones opened fire on Neo, Neo dodged almost all of the bullets but got hit by the final two. As Jones approached him in order to kill him, he held up his gun and said "Only Human", as he was about to fire, Trinity surprised him and shot him straight in the head. However, Jones wasn't dead, the shot only killed the SWAT pilot he possessed. So when the Agents possessed other SWAT soldiers, and reentered the room where firing at Morpheus since he was escaping. Although, Neo and Trinity managed to rescue Morpheus with Smith chasing them in hot pursuit, Jones and Brown ordered the Sentinel Strike on the Nebuchadnezzar.

Chasing Neo
Jones and Brown assisted Smith in chasing Neo. They were present when they saw Neo cornered by Smith at gunpoint. They also witnessed Smith kill Neo. After Brown confirmed Neo dead, the Agents were leaving when they saw Neo's resurrection. The three Agents immediately tried to gun him down, but Neo's powers as The One were revealed and he telekinetically stopped the bullets. When Smith attempted to fight Neo, Neo destroyed him from within, causing Jones and Brown to flee.

After Smith's Defeat
A while after Smith's defeat, The Architect had Agents Jones and Brown return to the Source, where they were most likely deleted, due to their incompetence in dealing with Neo, and their programming was recycled to create Upgraded Agents: Jackson, Johnson, and Thompson. Which possessed superior programming to deal with Neo.