Scully's fears about her pregnancy may not be unfounded...
Kathy McCready’s labour has run in to complications, and an emergency C-section is necessary. As her husband Duffy scrubs up, the doors are locked, and the attending Dr. Lev delivers an alien baby.
Later, Doggett introduces Scully to Duffy Haskell, who explains that his multiple-abductee wife was murdered by doctors after giving birth to an alien. Furthermore, his wife had contracted cancer after being impregnated by aliens, but was cured in a further alien procedure. Duffy gives them a file from Zeus Genetics, and an ultrasound proving his story.
After he leaves, Doggett points out that the case is similar to Scully's - except for the pregnancy, as he doesn’t know that Scully is expecting. Scully is angry he’s been reading her file.
Scully investigates Zeus Genetics, a medical clinic. She overhears a pregnant woman, Mrs Hendershot, telling Dr Lev that she no longer wants to be in his care. Fearing discovery, Scully ducks into a store room, to find it full of bottled alien foetuses.
Flashback: Mulder is telling Scully that she is barren because her ova were removed and stored in a government lab. Mulder found them and had them analysed, but they aren’t viable - Scully wants a second opinion. She consults her doctor, Dr. Parenti, who tells her that her ova may be viable, but she’ll need a donor - Mulder volunteers.
Back in the present, Scully phones Dr. Parenti, asking him to compare Kath McReady's ultrasound scans with her own. He is dissecting Kath's alien foetus.Visiting Parenti later, he reassures her that the scans are normal. As she leaves, she sees Parenti and Dr. Lev talking.
Skinner and Doggett confront Duffy about threatening letters he has been sending Mulder and Dr. Lev. He will be labelled as dangerous if he persists... but it seems that Duffy is actually working with Dr. Lev, who is worried that the FBI are investigating their story.
Mrs. Hendershot visits Scully to warn her that their babies are in danger.
Scully, Doggett and Skinner meet, and Skinner tells Doggett that Scully has requested a leave of absence. After Doggett leaves, Skinner begs the uncooperative Scully to tell Doggett that she is pregnant.
Scully and Mrs Hendershot visit Dr. Miryum at the Walden-Freeman Army research hospital. The doctor runs an ultrasound, which is perfectly normal - but Scully sees a video with another woman's name being played into the ultrasound machine... She is being deliberately misled. Mrs. Hendershot tells her they must leave immediately.
Doggett gets another Agent, Farah, to run a check on Duffy's fingerprints. They belong to David Haskell, who died in 1970. Doggett approaches Knowle Rohrer to find out Duffy's real identity. He is promised information, but suspects that Rohrer may be CIA. He tells Skinner of his fears - Skinner tells him to find Scully at the military hospital.
As Scully and Mrs. Hendershot sneak out of the military hospital, they are confronted by Rohrer and some marines, who say Doggett has sent them to rescue her. They're driven away, but Mrs. Hendershot goes in to labour. They separate the women, and sedate Scully.
When Scully comes round, Doggett tells her that Mrs. Hendershot's baby was normal. Scully is convinced the babies were switched, but Doggett doesn't believe her - the ultrasound tape was being recorded over.
In flashback, we see Scully telling Mulder that she hasn't conceived with his sperm.
In the present, Mrs. Hendershot's alien baby is being observed by Dr. Parenti and Duffy Haskell...