"He is still--"
-Agents Jackson and Johnson
Johnson, along with Agents Thompson and Jackson, entered the building where the Crisis Meeting was being held, forcing the Zion operatives who were present to withdraw. Neo fought Johnson to buy enough time for the other operatives to escape and discovered that he, along with his fellow Agents, were upgraded since he could block some of Neo's attacks. However, despite being initially caught off guard by the Agents' upgrades, Neo still managed to defeat all three of them with relative ease.
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 PlantEdit
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.