The season 8 mythology was all planned in advance -- unlike the first 6 years of the show. We are given pieces of the whole, but it's not before seeing the last episode that we get a clear picture of what is going on. In a predictable "Rosemary's Baby" (Polanski, 1968) turn of events, scribes Carter and Spotnitz take us to mysterious experiments with pregnant women and alien babies, raising concerns as to the nature of Scully's baby.

The flashbacks with Mulder

David Duchovny returns for some short appearances that please shipper fans. The flashbacks take place after the remission of Scully's cancer (5X03: Redux II), and given the closeness of Mulder and Scully most likely somewhere during season 7.

Mulder 'reveals' to Scully that he "found out the reason why you were left barren. Your ova were taken from you and stored in a government lab" (4X15: Memento Mori); this is a gross mistake: Scully had already learnt of that in 5X07: Emily when Mulder was pleading for Scully to be allowed to adopt Emily. Mulder: "I took them directly to a specialist who would tell me if they were ok. [...] The doctor said that the ova weren't viable." Scully said she wanted a second opinion, so she approached Dr. Parenti of "Parenti Medical Group". Dr. Parenti concluded otherwise and assured Scully a pregnancy would be possible. Given Dr. Parenti's involvement as we discover it in this episode, he probably lied about the ova being viable. Two years after Mulder stole them, the ova were definitively dead, probably as a result of Mulder taking them out of proper refrigiration for a short period. Dr. Parenti wanted to add Scully, unwittingly, in his experiments with alien babies. With Mulder as a donor, Scully went ahead with the attempt to be artificially impregnated. But according to Dr. Parenti, this attempt was a failure. Some time later, Scully got pregnant. With what she learns in this episode, doubts take ahold of Scully: what if Dr. Parenti did lie to her? What if he did attempt to impregnate her with what looks like an alien baby, and Mulder is not the father at all? (Retrospectively, this was nothing but a red herring.) Scully gives up on being monitored by Dr. Parenti and resumes her very stressful pregnancy. After a rough beginning of a partnership, Doggett learns of Scully's pregnancy; Scully kept it a secret because she was "afraid that they'd use it against me to take me off the X-Files so that I couldn't find Mulder".

Title note: 'per manum' means 'by the hand' in latin. What to do of this? Is this a twisted way to make reference to Mulder's activities after Scully asked him to be the father of her child? Mulder: "At that part, I'm a pro."

Duffy Haskel and Zeus Genetics

Threads are introduced but no answers are given yet. We learn that a certain fertility clinic, Zeus Genetics, does experiments involving what looks like alien babies. (The name Zeus Genetics is eerily similar to Zeus Storage, the company involved with the hybrids of 1X23: The Erlenmeyer Flask, but this is nothing more than a coincidence. Still, it's fitting for scientists playing God.) Zeus Genetics employs Dr. Lev and Dr. Parenti. "Dr. Lev is a serious physician, a leader in the field of birth defects. His peers hold him in the highest regard." The 'fetus room' of the Zeus Genetics offices displays many human babies with horrible birth defects, but the line between a deformed human fetus and an alien-like fetus is very fine. Indeed these fetuses could be waste results from previous experiments, before reaching a relative success with what looks like a fully alien baby being born (in the teaser); it dies soon after birth. For answers see 8X20: Essence / 8X21: Existence.

David Haskell was a Marine who supposedly died in 1970 ("buried in a Virginia cemetery, USMC honor guard ceremony"); after this, he began working for the government in some super-black program "in intelligence" under the name Duffy Haskel. Undercover, he was "president of the Ohio Mutual UFO Network" (MUFON) and had contacted Mulder in the past concerning "his wife's abduction experiences" "about eight years ago".

His dual role in the government and MUFON suggests he was working for the Syndicate (not unlike Diana Fowley, see 6X12: One Son), and him contacting Mulder must have been related to some attempt to manipulate the X-Files to spread false beliefs (5X02: Redux). Mulder must have seen it coming and did not investigate into their case (hence Haskell's threatening letters).

The women from MUFON (3X09: Nisei) are a good stock of test subjects for Zeus Genetics to tap on: abductees left barren, whose medical history is already known by the Syndicate. Kath was one of them. During all of his relationship with Kath, Haskell was undercover (Haskell presents her as his wife, but: Doggett: "I can't find any documentation that the two of you were even married"), and he used her in the projects he was truly working for. In league with Dr. Lev, Haskell took Kath to Zeus Genetics, where she was impregnated with what looks like an alien fetus. After delivering, Kath had become useless and knew too much, so she was killed off. Other MUFON women must have met similar ends. X-Files uses popular UFOlogy beliefs once again: abduction stories including sexual intercourse, impregnations and stolen newborns.

Mary Hendershot and Knowle Rohrer

The episode revolves around Mary Hendershot, another test subject of Zeus Genetics who distrusted her doctors and was ready to leave Zeus Genetics. Mary must have been a  MUFON member, and seeing that many of her fellow abductees were dying when giving birth, she was suspecting that something was wrong (when he tries to reassure Mary, Dr. Lev says "there are no similarities between your baby and the others"; also, Scully: "women just like her have been murdered in childbirth"). Dr. Lev and Duffy Haskell decided to use Scully and the X-Files to be able to follow Mary's pregnancy to its end. Haskell: "We still risk losing Hendershot." Scully: "It was all planned. [...] We were used to get at Ms. Hendershot's baby." They knew of Scully's history through Dr. Parenti. Haskell came to the X-Files and made stories up about his wife's experiences, presenting her experiences exactly like Scully's in order to raise her interest (Doggett: "The abduction the tests, a bout with cancer then a remission. [...] That's your story, Agent Scully. I'd say right down to a tee."). After teasing Scully, Haskell, through a MUFON connection with Mary, brought Mary to her ("a man named Haskell led her to me"), presenting her as another woman in danger. Scully takes her to where she considers she will be safe: the Walden-Freedman Army Research Hospital (where Mark Snow has a cameo as one of the doctors!). An Army hospital? Scully should have known better. The doctors there were in on the plot and would have brought Mary's pregnancy to term on Dr. Lev's behalf. Scully, now 14 weeks pregnant, has an ultrasound done to her;

she discovers the ploy when she sees that her ultrasound was not being recorded but was a pre-recorded tape on 'play' (from a Nancy Maxwell, dated 11/20/2000 -- let's not go into internal timeline coherence with Scully's pregnancy). Scully takes Mary and they flee again.

Mary ends up delivering in the hands of the team of Knowle Rohrer. He's an old friend of Doggett's ("You and I go back a long time. You know I'll do anything I can for you.") who seems pretty high in the US intelligence community. Doggett contacts him concerning Haskell's undercover nature. Knowle obliges and 'saves Scully and Mary's life' when he takes them safely away from the Army hospital. Still, Knowle does not let Scully witness the birth, and later on Mary is the sound mother of a healthy boy; Scully is convinced that "they switched it" and does not trust Knowle. Doggett doesn't know yet that Knowle is a Supersoldier (8X18: Three Words) and completed Dr. Lev's work with the delivery because Zeus is overseen by the Supersoldiers themselves (8X20: Essence). Scully was manipulated from beginning to end and now touches her womb with concern and fear.

Mulder: "Never give up on a miracle."