Agent Jack Thompson was one of the agents called by Roger Dooley to discuss the possible betrayal of Howard Stark to the United States. While talking to Sousa and Carter, Thompson interrupts because it has a job to Carter: sorting papers. The next day, Dooley sent Thompson, Krzeminski and Yauch to La Martinique to interrogate the owner of the place, Spider Raymond. When Thompson, Krzeminski and Yauch enter to Spider Raymond's office, they found the corpse of Raymond on the floor. Later, Thompson informs Dooley that Roxxon Refinery disappeared after an explosion.
The next day, he and Dooley went to Roxxon Oil Corporation Headquarters to talk with the president of the company, Hugh Jones. Dooley asks Jones if they could inspect the employees, to which Jones agrees. As Thompson could not inspect the women, Dooley then called Carter to inspect the women. After arresting Miles Van Ert, Thompson was responsible for questioning. During questioning, Van Ert was brutally beaten by Thompson.
A few days later, Thompson and Sousa went to Howard Stark's mansion to talk to Jarvis. After taking him to the New York Bell Company, Thompson was in charge of the interrogation. Jarvis was very calm during the questioning until Thompson suggested the possibility to deport him and his wife. When Jarvis was going to be questioned by Dooley, Carter pretends incompetence to free Jarvis. Dooley scolds Carter and asks her to apologize to Thompson, she apologizes to him but Thompson does not accept them.
After the Chief Dooley travel to Germany, Thompson was in charge of the SSR's offices in New York. His first order was that all agents investigate the death of Ray Krzeminski. After the speech, Sousa prepared to leave. Thompson then asked him where he was going, Sousa replied that find clues about the death of Krzeminski. Thompson was present when Sousa brought his star witness: a homeless veteran.
As the witness said nothing, Thompson had to intervene because the witness did not want to cooperate. After the witness gives them information, Thompson told Sousa that not all veterans returning from war for a hug.
As Carter managed to translate the message of Leviathan, Dooley rewards Carter leaving her join the team of Thompson. Thompson refuses but Dooley reminds him that it is he who is in charge. Despite his dissatisfaction, Thompson accepts Carter on his team. Arriving in Belarus, he and Carter meet with the Regiment 107th better known as the Howling Commandos. Overnight, they all share war stories, then they ask Thompson how he became a war hero. Thompson tells his story; but Carter notes that he does not tell the whole story.
The next day, the team infiltrates the Red Room Academy. Here they find a film projector which shows films with subliminal messages. They also found a little girl, in a moment of distraction she stabbed Dum Dum Dugan and killed Junior Juniper by a gunshot. Later, they meet two scientists called Ivchenko and Nikola who were imprisoned in the Academy. The team frees the scientists before the Leviathan soldiers appear. During the confrontation between them and Leviathan, Thompson was very shocked until Carter asked him to react. Later, he tells Carter the whole story and invites her to drink with him.
After learning that Peggy Carter was helping Howard Stark, Dooley sent Thompson to capture her. As Carter had defeated the other agents, Thompson asks her to surrender but she does not surrender; Carter instead hits Thompson. He and Sousa went to Griffith Hotel to catch Carter. They went to Angie's room to ask her some questions. As Carter was out of the room, Angie pretends to cry for the purpose of annoying Thompson and Sousa. Eventually, Thompson and Sousa captured and takes Carter to the New York Bell Company for questioning.
Agent Sousa was one of those responsible for interrogating Peggy Carter. He asked Carter to confess because she knew his interrogation methods; but she rejects this request. He was later present when Carter confessed the reason why she helped Howard Stark. Dooley then sends him and Sousa to investigate the building crossing the street. Thompson told Sousa his experience in Belarus. Thompson also told Sousa that if he sees the woman shoot to kill. Later, Thompson saw as Chief Dooley sacrificed himself to save the lives of their subordinates.
Carter, Thompson and Sousa went to a cinema theater where a slaughter had occurred. Here, Sousa found the container of Item 17 and accidentally inhaled it. He attacks Thompson and Carter before being knocked out. When she questions the motives of Fennhoff, Stark appears and explains what happened in Finow. Stark offered himself as bait to make Fennhoff appear. Thompson with Stark gave a press conference to announce that all charges against him had been dropped, Stark annoyed him by making him say a lot of flattering things about Stark. During the speech attempted to kill Stark.
He and Carter investigated from where came the shot but only discovered it was just a decoy to distract them and capture Stark. That same night, Thompson and the others arrived to Stark's secret hangar, but only discover that Stark had already taken off towards Manhattan. Carter informs him that Fennhoff escaped, immediately he is knocked out by Fennhoff. Upon awakening, he watched as Fennhoff brainwashed Sousa. However, Sousa pretends to be brainwashed to arrest Fennhoff. The next day, Senator Walt Cooper congratulates Thompson for arresting Fennhoff and informs him that President Truman wanted to talk to him.