Modeski left her position, but was soon listed by the FBI as armed and dangerous and prone to elaborate lies bordering on the psychotic. At a convention in Baltimore, she met John Fitzgerald Byers, to whom she introduced herself as Holly and claimed to be searching for her three-year-old daughter who had been kidnapped by her ex-boyfriend. Byers agreed to help "Holly" and hacked into a Department of Defense network and downloaded an encrypted file which Modeski claimed would help her find her daughter. With help from Melvin Frohike and Richard Langly, Byers and Modeski evaded her ex-boyfriend, who had managed to follow her to the convention. This man was none other than Fox Mulder.Realizing that they were dealing with someone more important than they previously thought, the three men hacked into the FBI mainframe and learned that Holly was actually Susanne Modeski. Modeski explained her story to them and how the Army had set her up. They then traveled to a warehouse, where they discovered the bioweapon-laden inhalers in several large crates awaiting deployment. However, Mulder arrived and tried to arrest Modeski and her three companions. Before this could be done, a pair of agents showed up and opened fire on the group. Mulder was doused with the hallucinogenic bioweapon and totally helpless as the two men came to kill him. Modeski shot and killed them both, saving Mulder's life before she fled the scene.
Moments later, a team of operatives led by X appeared and cleaned up the area, erasing all evidence of any unusual activity. When confronted by Byers, X aimed a gun at his head and fired - but there was no bullet. Confident he had intimidated them enough, X left, but not before declaring that Mulder remain unharmed.
Modeski fled in Mulder's car, which she left at a train station before going to the local major newspaper. However, the writers did not believe her story. Byers and his companions met with Modeski outside the newspaper building, and she exhorted them to use their quest for the truth as a weapon against the sinister government conspiracy in which she was involved. As she walked away, a black car appeared rapidly and Modeski was apprehended by X. (TXF: "Unusual Suspects")
After that incident, Modeski was operated on, but soon after saved by Grant Ellis. They would eventually become engaged by 1999. Modeski believed that Ellis wanted to work against the project to develop the mind control drug Analytic histamine and eventually sabotage it and run away with her.
In 1999, Modeski joined DefCON, the Defense Industry's annual conference in Las Vegas, but under Ellis' name. She was surprised to find Byers at her hotel door, wanting to rescue her. She explained that, despite her shaky loyalty to the government, she was too valuable to them to be killed. She also explained Ellis to him. She later got into the hotel room he was staying in with the The Lone Gunmen and explained about the project and her intentions to leave it. Modeski found out her room was actually spied on, first, and that things were not what they seemed. She recognized Scully's condition when Frohike brought her there, and realized her project's drug was being used illegitimately. She had the antidote and cured not only Scully but Langly as well, allowing them to plan a fake shooting of Modeski to expose Ellis. Modeski confronted Ellis in the hotel room with the Lone Gunmen, though that was interrupted and Ellis was killed.