Summary: Hosteen is voicing over again, this time about animals being symbolic to the Navajo. Mulder’s recovery reminded them of the Gila monster, which healed a man by putting his parts back together. Lightning and thunder brought him back to life. After Mulder was better, the Navajo learned from other tribes that something big had happened. He tells the story of White Buffalo Woman, who taught Native Americans how to live virtuously and pray. Then she turned into a white buffalo and returned to the heavens. The day Mulder was healed, a white buffalo was born, an omen that big changes are coming.
Back in Mulder’s apartment, Scully and Skinner are still facing off. He insists that he’s trying to help her, but he’s not about to put down his weapon. Fortunately, Mulder arrives to serve as Scully’s backup. Skinner finally gives up his gun, and Scully explains that she was warned that someone she trusted would try to kill her. Skinner shows them the recording, which Mulder says CSM killed Bill over. Mulder says, “I was a dead man. Now I’m back,” which would be a great tagline for a probably bad movie.
Mulder explains what’s on the cassette, then tries to make Skinner give it to Scully. Skinner points out that it’s the only leverage they have against the conspirators, so they need to protect it. Mulder backs down and takes Scully away to search out more truths. She tells him that she assured Teena that he would be okay, even though she had no proof she was right. She just knew. Meanwhile, Maggie arrives at the hospital where she thinks Scully has been brought in. She’s shocked to hear that Melissa’s the daughter who was shot. She’s in an induced coma, and the doctors can’t do anything more for her except monitor her.
Scully and Mulder take the picture of Bill and the conspirators to the Lone Gunmen. Byers brings up Operation Paper Clip, a World War II agreement with Nazi war criminals that gave America access to their scientific knowledge. Langly IDs a man in the picture as one of those war criminals, Victor Klemper. He experimented on Jewish people, and some of his tests led to space travel. Byers notes that the picture was taken in 1973, but Operation Paper Clip was supposed to have ended in the 1950s, which means there’s yet another secret the American government has been keeping. Langly reports that Klemper is alive and still living in the U.S.
Frohike arrives, happy to see Mulder alive. He gives Scully the news that Melissa’s in the hospital, and she immediately realizes that her sister’s shooting was meant for her. Mulder talks her into staying away from the hospital. CSM and his Syndicate have realized their mistake (well, Krycek’s mistake), and WMM wants to know who will fix it. He warns that Scully believes that Mulder is still alive. CSM is sure he’s not, and still has his buddies snowed that he has the cassette. They question that, asking to see the tape. CSM claims it’s someplace safe, but he’ll bring it to them tomorrow.
Mulder and Scully find Klemper in a greenhouse, and after some blathering about history, he’s all, “We did good work! So what if innocent people died?” Mulder thinks Klemper knows why Bill was killed. Klemper replies that it was probably in their best interest. Mulder shows him the picture, but Klemper hesitates to reveal any more truths. The only help he’ll give is asking if Scully knows the formula for Napier’s Constant, then revealing that the photo was taken outside the Strughold Mining Company in West Virginia. They’re on their own for the rest.
As soon as the agents leave, Klemper calls WMM to tell him that Mulder visited, but Klemper didn’t tell him anything. Now the Syndicate knows that Mulder is alive. Maggie spots a man in a suit outside Melissa’s hospital room, then gets a visit from Hosteen. Scully sent him to comfort Maggie in her place. Maggie allows him to pray for her daughter, who she thinks is getting better. Mulder and Scully head to the now-abandoned Strughold facility, which holds a bunch of doors that can only be opened by keypad codes. Napier’s Constant, 27828, opens one of the doors. Before Mulder goes through it, Scully wants him to think about the possibility that they might discover something bad about Bill.
Skinner summons CSM to the FBI building to report that he may have found the tape. However, it could have fallen into other hands. CSM isn’t interested in making a deal. He gets more and more frustrated as Skinner stays calm, saying they’ll talk again. Skinner, basically: “I know you do bad things.” CSM, basically: “Then maybe I’ll do bad things to you.” Mulder and Scully go underground, finding a tunnel full of file cabinets. The files all seem to be medical, and are helpfully stored in alphabetical order. In each one, Scully finds a birth certificate, smallpox vaccination certificate, and old tissue collection cassette.
Mulder asks what year Scully was born, then looks up her file. The tissue sample is recent, judging from the plastic container used. Mulder then looks for Samantha’s file, discovering that the label with her name has been placed over a label with his name – the file was originally his. The lights suddenly go out, and Mulder runs out of the tunnel to the front of the building. The windows are full of lights. In the tunnel, Scully sees something alien-like skittering around. As she runs away from it, Mulder runs out the back of the building in time to see a large spacecraft flying over it. Scully sees another alien in the tunnel, standing in front of more light.
Cars approach the building, so Mulder goes back in to retrieve Scully. He dodges bullets on his way back to the tunnel and reunites with his partner. She’s found a way out, and they’re able to escape the building undetected. In the morning, Skinner meets them at a diner in Craiger, Maryland, and tells them he has a plan to protect them: He’ll turn over the tape and get them reinstated at the FBI. Mulder refuses to give up the cassette even if it means saving his own life. He thinks the tape holds an explanation for the records they found.
Skinner wonders what Mulder’s hoping to find. Mulder replies that he wants to know why Bill was killed, what happened to Samantha, and why Scully was targeted. Scully, however, is on Skinner’s side – she would rather be safe and see Melissa than get answers that only Mulder wants. Since Skinner hasn’t been able to copy the tape, they’ll have to hand over the only version they have. Skinner promises to turn state’s evidence if his deal isn’t honored. Mulder lets Scully have the final vote in the matter. She tells Skinner to make the deal but not hand over the tape until Mulder okays it.
The agents leave the diner together as Hosteen voices over that he prayed for Melissa for two days. She improved, but Hosteen learned that the white buffalo calf stopped nursing. Then the mother buffalo died. Hosteen knows that sometimes, one creature must be sacrificed so another can live. Skinner arrives at the hospital with a message from Scully so her mother knows she’s all right. The man in the suit is still outside Melissa’s room, and Skinner decides to find out why. He chases him to a stairwell, where he and the man engage in some hand-to-hand combat. Krycek joins in, beats on Skinner a little, and steals the cassette.
Krycek and his criminal buddies then stop at a convenience store in D.C. to get some drinks. Krycek’s left alone in the car, growing suspicious when the other guys stop to look at him from the store’s doorway. He notices that the dashboard clock is flashing 12:00. Unlike on a VCR, where this meant that you didn’t know how to set the clock, Krycek realizes that this means his life is in danger. He takes off running as the car explodes. His buddies should be a lot more worried about how they’re going to explain this to CSM.
Mulder and Scully return to Klemper’s greenhouse, but instead encounter WMM. Klemper’s dead, and Mulder knows it wasn’t due to a bad heart. He recognizes WMM from the photo. WMM tells them about the spacecraft found in New Mexico in 1947 and the body retrieved from it. Mulder puts together his talk of Joseph Mengele with his mention that Klemper made flower hybrids to figure out that Klemper was trying to create a human-alien hybrid. The bodies in the boxcar in the desert were his failed human test subjects.
Scully denies that the technology was available; DNA wasn’t even identified until 1944. WMM says that Bill was in charge of collecting genetic data on Americans in case they needed to be identified in the event of nuclear holocaust. Mulder realizes that, due to the DNA samples collected from people who received smallpox vaccinations, Klemper had access to every person’s record from 1950 forward. Scully thinks WMM is just making stuff up, but WMM says he has no reason to lie. Scully, basically: “Whatever, Nazi.” Mulder notes that Scully’s file was in the mine – the records are of abductees.
Mulder asks WMM why Samantha was taken. WMM explains that Bill threatened to expose the project, so Samantha was taken as insurance. Mulder wants to know why he wasn’t taken. WMM can’t say, but he warns that Mulder’s still in danger for threatening to expose the project: “You have become your father.” Mulder wonders why WMM has told him all this. WMM replies that Mulder wanted to know it, didn’t he? He says there’s still more – more than Mulder will ever know.
Krycek calls CSM to report that he’s alive and has the cassette, but CSM will never find him. CSM reports to the Syndicate that Krycek is dead and the cassette was destroyed in the car explosion. He’s still going to meet with the FBI, even though there’s no deal to make. Mulder goes back to his mother’s house to find out if Bill ever asked her if she had a favorite child. Teena says she couldn’t choose – it was Bill’s choice. She always hated him for it, and still does, even after his death.
CSM meets Skinner in his office, hiding his amusement when Skinner bluffs that he has the cassette. Skinner promises to hand it over after Mulder and Scully are reinstated. CSM knows Skinner can’t make the deal, so he suggests a few ways Skinner’s life might end. Skinner calls in Hosteen and announces that there’s a new deal: If anything happens to Mulder or Scully, Hosteen will reveal everything on the tape, which he’s memorized. (He’s also, in the Navajo storytelling tradition, told it to 20 more Navajo.) “Welcome to the wonderful world of high technology,” Skinner gloats.
But we don’t get a happy ending: Scully finally made it to Melissa, but the damage from her shooting was too extensive and Melissa didn’t survive surgery. Scully laments that her sister died for her. She now agrees with Mulder that there’s no justice, though Mulder thinks they’re dealing with something bigger: fate. They’ve both been reinstated at the FBI, and though they’ve both suffered recent losses, they want to go back to work. Mulder thinks they can still find truth through the X-Files. Scully tells him she’s heard the truth – now she wants answers.
Thoughts: I guess I should call CSM and his buddies the Consortium, but apparently the Syndicate is used a lot. Also, it’s just easier to type.
I tried to look up Napier’s Constant, but I found a bunch of math and it made my head hurt and I had to take a nap.
For the record, Samantha’s tissue cassette is plastic, which means the sample was taken more recently. Make if that what you will.
'90s Flashback 
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