Suddenly, he seems to have some sort of adverse reaction from the sting and he plunges from his high position on the pole and lies dying on the ground as the boys look on. Without ever saying a word, the five boys walk off "You mean colonization," Mulder says. "Hegemony...a new origin of species," is Jeremiah's reply. Mulder takes a better look through binoculars, he sees a young girl who looks exactly like an eight year old Samantha. "That's not possible. She's no older than the day she was taken." X says, "Don't unlock doors you're not prepared to go through. Protect the mother." Distracted by the threat from behind, he fails to look at the opening door of the elevator and turns just as three shots are fired by the Gray-Haired Man. With multiple shots to the chest, X lies dying in the hall. As he turns to go, he opens a folder she's handed him, and inside is a picture of several of the Samantha clones working on the farm. He turns, and Marita says, "Not everything dies, Mr. Mulder."

Herrenvolk (part 2 of 2) The episode opens with a telephone lineman climbing a utility pole on a deserted stretch of road in Alberta, Canada. A bee stings him on the neck and as he swats it and it falls to the ground, he looks down to see five identical blonde boys looking up at him. He addresses them but they don't answer, simply staring at him in with no expressions on their faces. Suddenly, he seems to have some sort of adverse reaction from the sting and he plunges from his high position on the pole and lies dying on the ground as the boys look on. Without ever saying a word, the five boys walk off into the rolling hills. We return to the nighttime stand-off at the mill that Mulder, Scully, and Jeremiah had met at. The Alien Bounty Hunter is approaching the group with his ice-pick weapon drawn. Jeremiah suddenly breaks formation and runs into the workings of the silent mill. Mulder shouts a warning against shooting the ABH to Scully before heading after JS. The ABH barrels past Scully in pursuit of Jeremiah and a long, long chase scene ensues. Mulder is chasing down JS and the ABH is chasing down JS, and at one point the ABH runs into Mulder and simply turns away and continues his pursuit, interested only in JS. Mulder finds JS and together they try to evade capture. Scully runs to start the car for them to get away when the ABH jumps onto the hood and she lays on the horn to warn the others against approaching the car. Mulder leads Jeremiah out of the building to the piles of wood chips and the ABH follows. As he searches the grounds, Mulder suddenly rises up from a pile of wood chips and sinks the alien ice-pick into the ABH's neck region. As green fluid oozes out, the ABH falls down with the weapon sticking out of his neck and ceases movement. The ABH has dropped his own weapon, which Mulder picks up as he searches for JS. Meanwhile, Jeremiah has found a small boat and is trying to flee until Mulder stops him and entreats him to turn around, telling him that he needs his help to heal his mother. Scully arrives just in time to see them depart together on the boat and, though she shouts after them, they appear not to hear her and disappear. She returns to the body of the ABH and as she check for signs of life, he suddenly grabs her by the throat and demands to know where Mulder and JS have gone. Maybe Mulder's aim with the weapon wasn't so good... Jeremiah tells Mulder that if they go to the hospital, "they" will be waiting for him and will kill him. Mulder says, "What can they do? We're working in the light." Sort of a naive statement coming from Mulder. Jeremiah tells him that he will be eliminated since he is inconsequential to the larger plan. "You mean colonization," Mulder says. "Hegemony...a new origin of species," is Jeremiah's reply. Jeremiah tells Mulder he can show him what he means, and show him his sister. This gets Mulder's attention. We see CSM at the hospital, holding Mrs. Mulder's hand as she lies unconscious. The Italian Elder and the Gray-Haired Man join him and wonder why Jeremiah and Mulder haven't shown up as expected. The Elder feels there has been a security leak and his proof is in some pictures he has come into receipt of; pictures of CSM and Mrs. Mulder at the summer home. They decide to plant evidence and see who takes the bait. The bait will be a threat to Mrs. Mulder's life...that her life is in danger, and that she is unprotected. We see Scully sitting in her car at the mill the next morning. Mulder calls her on her cell phone and tells her that people will be looking for him since he stole a car from an airport in Alberta. He wants her to cover his tracks and just wanted to let her know he was okay. Unfortunately, the ABH was holding Scully hostage and has overheard the conversation so now knows where Mulder is. The ABH releases Scully and heads off as she warns Mulder of his intentions..."The man you left for dead is still alive." Mulder and Jeremiah run out of gas 10 miles from their destination so hoof it, stumbling upon the body of the dead lineman on the way. Jeremiah warns Mulder not to touch the body and Mulder gets no reply from JS when he says, "You know what killed him, don't you?" The body is incredibly decomposed in the 24 hours since the man's death. They finally crest a hill and look down onto a farm where rows and rows of plants are growing under canopies. "You're looking at the future, Mr. Mulder. A flowering shrub not found on any taxonomic chart." JS says it's being grown for the pollen, and as Mulder takes a better look through binoculars, he sees a young girl who looks exactly like an eight year old Samantha. "That's not possible. She's no older than the day she was taken." Meanwhile, Scully is called into Skinner's office where he demands a report of their progress on the investigation into JS. He tells her that he's tracked down the multiple Jeremiah Smiths working for the Social Security Office and none of the five has showed up for work...all are missing. He also had Pendrell download the files from the Smiths' workstation computers and they've found a huge catalogue of entries that are not Social Security business. The entries total around a billion, with each line of information consisting of the letters SEP followed by a string of 20 letters, then another group of 15 alpha-numeric characters. Scully takes a printout to work on its meaning. Scully heads to Mulder's apartment where she puts the masking tape X in the window and sits to wait, working on cracking the mysterious codes to pass the time. X finally shows up but only wants to talk to Mulder. He says he has information that will greatly concern him regarding his mother. "She is unprotected." Scully asks him about the entries she is analyzing and what SEP means. "You're going in the wrong direction," he tells her, but she pressures him and he tells her it stands for smallpox eradication program. Scully wonders why smallpox and X says, "Don't unlock doors you're not prepared to go through. Protect the mother." Back on the farm, Mulder runs through the rows of plants to the girl who so resembles Samantha. The girl doesn't speak or respond to him and JS tells Mulder that she has no language. She's a drone, a worker. They walk to a nearby compound where Mulder sees many "Samanthas" as well as multiple blonde boys. Jeremiah tells him they are a workforce made up of clones, serial ovotypes. He says they can't stay any longer and goes in search of gasoline for their car. As they prepare to leave, Mulder takes the hand of the first Sam clone and starts to bring her with them. JS resists, saying that Mulder has a chance to comprehend something so much bigger, "to expose it." But Mulder doesn't understand and demands that JS explain it to him. You have to wonder what the heck they talked about on the plane trip, the drive, and the 10 mile walk! Before he can reply, the ABH comes careening onto the scene in a speeding car and JS, Mulder, and the Sam clone run. Sam leads them to an apiary where the bees are kept. Mulder asks if the bees killed the lineman and JS says they will kill Mulder too since he has no immunity. Pouring the gasoline over his body, they all enter and find themselves in a high-ceilinged shelter full of huge stalactites of honeycomb. Unfortunately, the way in is the only way out and they are trapped as the ABH enters behind them. They knock some honeycomb off the ceiling which knocks him to the floor and, as he's swarmed with bees, they abandon him and escape. Scully shows Pendrell the progress she's made, telling him that the 20 letter code is made up of amino acids, the building blocks of protein. They represent variants of a cowpox virus used to inoculate against smallpox. They think the 15 digit code in the files represents a number used to inventory everyone inoculated. When they take this and further evidence before an FBI special committee, Scully is told that it sounds more like something they would expect from Mulder. But Scully is confident that science backs her in her findings. She has taken a biopsy from her smallpox scar as well as Pendrell's and they find evidence of a protein tag applied at the time of inoculation. Skinner asks by whom and to what purpose, but other than a government agency, Scully has no idea who or why and it seems JS is the one with the answers. Mulder calls Scully and says that he and Jeremiah are on their way back "with someone else" but need protection when they arrive at the hospital. Scully says that will be no problem since lots of people want to talk to Jeremiah. As Mulder hangs up the phone, the ABH makes the scene and smashes his car through the phone booth just as Mulder dives for safety. He picks up Mulder from the debris as Mulder begs him not to kill Jeremiah, that he needs him to heal his mother. "He shows you only pieces, not the whole. He's a traitor to the project," says the ABH. As Mulder offers his life instead and continues to beg, the ABH says, "Everything dies," as he tosses Mulder into the side of the car. Jeremiah limps away from the accident as the ABH draws his weapon and enters the car to kill the Samantha clone. At the hospital, Skinner is getting impatient and Scully knows something is wrong since Mulder is five hours overdue. Just then, Mulder staggers in, battered and incoherent, in shock. He enters his mother's room and breaks down as Scully holds and comforts him. We see the interior of Mulder's apartment with an X fixed onto the window and a shadow of someone inside. X exits the elevator and walks to Mulder's door but when he finds the door ajar, he's suspicious and walks back to the elevator. Distracted by the threat from behind, he fails to look at the opening door of the elevator and turns just as three shots are fired by the Gray-Haired Man. With multiple shots to the chest, X lies dying in the hall. Back at the hospital, Mulder and Scully sit with his mother as Mulder regrets how close he came to being able to save her. He tells Scully how he saw his sister. "I've seen too many things not to believe." Scully says they have some answers and that there's hope in that, but Mulder can't see how she puts so much faith in her science since science can't explain what he's seen. "Nothing happens in contradiction to nature, only in contradiction to what we know of it," she responds. She tells him she was warned by a man they both know, who she believes knows the truth. Someone who can lead them to a place to start. Cut to X, dragging himself down the hall, blood streaked out behind him. As he makes his way to Mulder's doorway and collapses, he scrawls the letters "SRSG" in his own blood before he dies. Some time has passed as Mulder is met in the outer office of the Special Representative of the Secretary General in the UN building. Marita Covarrubias, the SRSG's assistant, introduces herself and says that the SRSG has been called away. Mulder tells her he's contacted multiple SRSG's about the farmland in Canada and has yet to get any answers. She says the farm was abandoned but they do know the plants were ginseng. No evidence of bee hives or bee husbandry was found. She asks Mulder why this is so important to him, and he gets choked up saying that he's had some personal losses and was hoping he could get some answers. As he turns to go, he opens a folder she's handed him, and inside is a picture of several of the Samantha clones working on the farm. He turns, and Marita says, "Not everything dies, Mr. Mulder." We see the ABH arriving at Mrs. Mulder's hospital room where CSM is waiting. "I need to know the reason for this," he says to CSM. CSM tells him it is so the work can continue without interference from Mulder. If the mother died..."The fiercest enemy is the man who has nothing left to lose." One has to wonder if this applies to Mulder, or to CSM himself. Then CSM adds, "And you know how important Agent Mulder is to the equation." The ABH nods, then leans down and rests his palm on Mrs. Mulder's forehead as a look of calm and concentration overcomes him. Mulder's mother opens her eyes and her gaze shifts to CSM who watches silently.