Thompson, along with Jackson and Johnson, intruded into the Crisis Meeting and fights Neo. During the fight, Jackson and Johnson were defeated by Neo and Thompson fought against Neo alone. Due to Neo having powers of the One, he was able to defeat the three agents in under one minute.
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, 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.
Agents Thompson and Johnson manifest inside a police cruiser to chase Trinity to the freeway to stop the Keymaker during The Freeway Chase. When Johnson's attempt to kill Trinity failed, Agent Thompson pulled alongside Trinity's vehicle in an attempt to kill her. After Trinity escapes, Thompson and Jackson inform Johnson, who is standing on a bridge waiting for the Keymaker.
Ambush at the Nuclear Power PlantEdit
Thompson appeared one final time at the Nuclear Power Plant to kill Trinity and stop her from reaching her Exit after helping 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, Thompson and Trinity are shooting at each other with their guns trying to kill one another. However, Thompson succeeds by shooting a bullet just below her heart. Before Trinity falls onto the car below, Neo manages to save Trinity and 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.