The episode begins with Morris Fletcher (Michael McKean) on a boat in the Bahamas, where he is accosted by armed men and his vessel is blown up. When he is rescued and detained, he approaches FBI agents Monica Reyes (Annabeth Gish) and John Doggett (Robert Patrick) with information related to the Super Soldiers in exchange for his release. Doggett and Reyes turn to The Lone Gunmen when Fletcher provides an alleged photo of the Super Soldier, whom the Gunmen recognize as Yves Adele Harlow (Zuleikha Robinson), a fellow hacker who went missing a year ago. The Gunmen refuse to believe the evidence, especially when they find that Fletcher provided it, although the agents continue to pursue the trail.
Meanwhile, Harlow murders a biology professor, cuts out an organ and disposes of it in a furnace. After the Gunmen capture her, she reveals that he had been experimenting with the immune system of sharks and had been grafting pieces of shark onto his body in order to become a living host to a biological weapon. His research had been funded by Harlow's arms dealing father, who had commissioned Fletcher to find her and prevent her from stopping his biological terrorism plot. She further informs them that there is another host, whom she is trying to identify and locate before he can unleash his deadly payload.
Once Fletcher realizes that he has been used by Harlow's father, he teams with the Gunmen to help her find the second bio-terrorist. After a few false starts and chases, the Gunmen corner the bio-terrorist with only a few minutes before his virus is due to be released. They realize that they lack the time to destroy his virus-filled organ and therefore pull a fire alarm, causing large emergency doors to seal shut, simultaneously containing the virus and entrapping them with it. Their sacrifice earns them a final resting place in Arlington National Cemetery, where Fletcher, Doggett, Reyes, Harlow, Dana Scully (Gillian Anderson), Walter Skinner (Mitch Pileggi), and Jimmy Bond (Stephen Snedden) pay their respects to them
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