Thompson, along with Johnson and Jackson, attacked the Crisis Meeting and fought Neo who held his ground and gave the other redpills enough time to reach their exits. During the fight, Jackson and Johnson are knocked out and were separated from Thompson, leaving him to fight Neo alone momentarily. However, Thompson was not able to defeat Neo and he was the last one to be eliminated out of the three by being kicked across an alley and into a lamppost. Eventually, with the powers of The One, Neo defeated them in under one minute and escaped.
Thompson reappeared during Neo's battle with Smith and his clones. After taking possession of a bluepill who was witnessing the fight between the many Smiths and Neo, he is almost immediately confronted by a Smith before he could interfere with the battle, and immediately recognizes him ("You!"), to which Smith starts to copy over the Bluepill. Once Thompson is taken over and is another Smith, the two Smiths join the fight and Agent Thompson appears to have been destroyed. However, though Smith did copy over the Bluepill that Thompson had taken over, he did not actually copy over Thompson's own code, so Thompson still exists within the system.
In an attempt to kill Trinity and The Keymaker during The Freeway Chase, Agents Johnson and Thompson took possession of two police officers and joined the chase. When Johnson's attempt to kill Trinity failed, Agent Thompson pulled alongside Trinity's vehicle in an attempt to kill her. Trinity rams his police car into some water barrels. After Trinity escapes, Thompson and Jackson inform Johnson, who is standing on a bridge waiting for The Keymaker.
Later, Thompson possesses a truck driver to block Trinity. Somehow, he also appears with Agent Jackson in another police car. He instructs Jackson to "find the exile".
Later on, he jumps back into the truck driver to meet Johnson in a head-on truck collision.
Ambush at the Nuclear Power Plant
Thompson made his final appearance at the Nuclear Power Plant in an attempt to stop Trinity after she helped Neo reach The Architect. During his fight with Trinity, Jackson appeared and the two Agents tried to kill Trinity with their weapons. To escape, Trinity jumps out through the building window and Thompson follows her.
As both of them fall, Trinity and Thompson are shooting at each other. However, Thompson ends up succeeds by shooting a bullet just below Trinity's heart. Before Trinity falls onto the car below, Neo manages to save Trinity while Thompson falls to his temporary death by landing on the car.
- Shortly before Thompson was assimilated by Smith, he says "you" in a slightly fearful and angered tone. This implies that Thompson not only knew of Smith, but seemed either fearful of what he was capable of or surprised that he was still in the Matrix despite being an Exiled Agent.
- During the Freeway Chase sequence, Thompson can be seen reloading his Desert Eagle (although he never fires it again after that). Reloading is not a very common sight in The Matrix Trilogy. Also, he can be seen thumbing away at the safety for his firearm, a rare sight in any action film.