When scam artist Morris Fletcher claims to know the identity of a super soldier, Reyes and Doggett turn to the Lone Gunmen for help.
Morris Fletcher charms a beautiful, silly woman aboard a yacht in the Caribbean, pulling at the knot securing her bikini top. Suddenly, three Bahamian men board Morris� boat, abduct the girl and set fire to the boat. Morris dives into the water moments before a massive explosion destroys the craft. Fluttering down in the debris are schematics for a flying saucer.
The Coast Guard rescues Morris, who requests Reyes and Doggett�s presence. Morris claims to have been freelancing for a foreign billionaire, after convincing him that the Air Force lost a UFO over the Bermuda Triangle. In reality, Morris was only interested in cruising the Bahamas. The agents don�t believe his story and begin to leave, but when Morris claims to have information about a female super soldier, they grow more interested.
Reyes and Doggett show up at the Lone Gunmen offices with a photograph of Morris� alleged super soldier. The stunned Gunmen immediately identify her as Yves Adele Harlow, a fellow hacker who disappeared a year earlier, and refuse to believe the tale about her being a super soldier. They are outraged when they realize Morris�a scam artist who used them to track down Yves once before�is behind it all. But Reyes and Doggett are less reluctant to dismiss Morris� story.
Meanwhile, Yves enters the office of biology professor Houghton, fires a futuristic-looking pistol at him, then disappears out a window. A college administrator finds Houghton�s body, a gaping wound across the middle of Houghton�s chest. Yves uses a furnace to incinerate an unidentified human organ vacuum-packed in plastic.
Tipped off by Jimmy Bond, the agents speak with the college administrator, John Gillnitz. He explains that Houghton was a marine immunologist experimenting with the remarkable immune system of sharks.
A medical examiner tells Reyes and Doggett that he discovered some type of cartilage grafted into Houghton�s body. With Kimmy the Geek�s help, the Gunmen locate Yves inside a hotel, apparently stalking a bald man. The Gunmen rush into the man�s room, alerting the apparent victim, who rushes outside and escapes. The Gunmen handcuff Yves, only to be told that she�s no super soldier, and unless she�s allowed to finish what she started, innocent people will die.
The Gunmen realise that Morris is wearing a homing device, which he planned on activating once he found Yves - who he was out to find from the very beginning, at the behest of Yves� father, an international arms dealer and "scum of the earth." Yves explains that the man she killed was a terrorist whose research was funded by her father.
Houghton had developed a means of keeping himself alive after having been infected with an engineered virus. Only one other such terrorist remains alive - the bald man Yves tried to kill. Carried within him is a virus-filled vessel which will decay at precisely eight o�clock that evening.
The Gunmen are able to determine where the bald man is headed, but once captured extensive medical testing can find no sign of a virus-carrying vessel within his body.
Morris realizes that the bald man is a decoy, leading Yves to conclude that the other man carrying the virus is John Gillnitz, who is about to attend an international bioethics forum at eight o�clock that evening. She, Jimmy and the Gunmen race to the forum with only minutes to spare. Jimmy calls out Gillnitz�s name, causing him to leave his seat and make his way to a far exit. The Gunmen and the others give chase. With only a couple of minutes to go before the virus breaks out, the Lone Gunmen corner Gillnitz in a room. Realising that there�s not enough time to remove the vessel, they pull the fire alarm, so sealing the room and sacrificing themselves.
The episode ends with Scully, Reyes, Doggett, Skinner, Morris and Kimmer standing in Arlington Cemetery at the funeral of the Lone Gunmen. Scully says that world was a better place for them having been in it.