Jackson, along with Johnson and Thompson, intruded the Crisis Meeting and fights Neo while Neo is giving the other redpills enough time to reach their exits. During the fight, Thompson and Johnson are knocked off their feet and were separated from Jackson, leaving him to fight Neo alone momentarily. However, Jackson was not able to defeat Neo and he was the first one to be eliminated out of the three by being kicked high into a brick wall. Eventually, with the powers of The One, Neo defeated them in under one minute and escaped.
In an attempt to kill Trinity and The Keymaker during The Freeway Chase, Agents Jackson and Thompson took possession of two police officers and joined the chase. After the Keymaker was helped onto a semi truck by Morpheus, Jackson relocated the Keymaker's position. Agent Johnson picked up on the signal and jumped off an overpass onto the semi truck that the two were riding on to try and kill the Keymaker.
Ambush at the Nuclear Power Plant
Jackson made his final appearance at the Nuclear Power Plant in an attempt to stop Trinity after she helped Neo reach The Architect. Agent Thompson was already inside and fighting against her. During the fight, Trinity fled but was surprised that Jackson joined in and started to fire at her with his weapon. After Trinity jumped out of the building's side window, Thompson followed her while Jackson remained inside the building .
Enter the Matrix
Jackson dispatched a group of SWAT team in order to pin down Ghost and the rebels of the Vigilant at the Airport. He also took control of a chopper trying to kill Ghost but was later shot down. Jackson chases Niobe in an underground tunnel at the airport while she was attempting to rescue Axel. Jackson also attempts to kill Niobe and Ghost after the crew of the Caduceus is saved but the two were unexpectedly saved by The Keymaker.