Then you are meant for one more thing: Deletion.”
― Johnson to The Keymaker during The Freeway Chase.[src]
Johnson, along with Thompson and Jackson, attacked the Crisis Meeting and fought Neo, who held his ground and gave the other redpills enough time to reach their exits. Johnson is the first to attack, but when Neo dodges his attack, the other two join in. During the fight, Neo uses Thompson as support while kicking Johnson off his feet, over some stairs, and into a wall. Johnson is the second Agent eliminated in this battle. Eventually, with the powers of The One, Neo defeated them in under one minute and escaped.
In an attempt to kill Trinity, Morpheus, and The Keymaker, Agents Thompson and Johnson took possession of two police officers and joined the chase. Johnson jumped onto the car Morpheus, Trinity, and The Keymaker were in, in an attempt to apprehend and delete the Keymaker. However, after dodging bullets from Morpheus' machine pistol with the aid of one of the Twins, Johnson was thrown off when Trinity braked suddenly.
Not too long after, he was informed about where Morpheus and the Keymaker were and, after taking possession of another police officer on a nearby overpass, immediately jumped to the semitrailer Morpheus was on and engaged him in combat. Despite Morpheus putting up more of a fight than Johnson expected, Johnson's upgraded combat abilities allowed him to quickly gain the upper hand and defeat Morpheus, knocking him off the truck.
After this battle, Johnson assumed that Morpheus was dead, and informed the Keymaker that he is no longer necessary to the Matrix and was about to delete him. Unknown to Johnson, though, Morpheus survived his fall by landing on the hood of the car driven by fellow Zion operatives Niobe and Ghost.
With Johnson's attention focused solely on the Keymaker, Morpheus got back on the truck and launched a suprise attack, kicking Johnson off the truck and into an oncoming car. Johnson possessed the driver of the semitrailer that Morpheus and the Keymaker were on while Thompson took control of another, oncoming truck to ram Johnson's semi in an attempt to kill Morpheus and the Keymaker, who were still on top of Johnson's truck. However, Neo managed to fly in and save them at the last minute.
Ambush at the Nuclear Power Plant
Johnson, along with his Agents, tried to stop Niobe and Ghost from blowing up the power plant. Ghost fought off Johnson, who was electrocuted by a damaged and sparking computer server.
Behind the Scenes
His line right before attacking Neo, "Only Human", raises the possibility that Johnson was an upgraded version of Agent Jones from the prior film due to the similar delivery of the line.