The first one was from character Sveta (played by Annet Mahendru) who tells Dana Scully and Fox Mulder "they take the babies before they are born".
This young lady claims to have been implanted with fetuses that are taken from her, repeatedly. She also, in this Episode One, tests positive for alien DNA.
The second theme, reiterated and in a somewhat different setting in Episode Two, is women as incubators. Discovering a clandestine program supposedly to help young women with deformed babies, and funded by a wealthy patron, Scully reflects back on her own pregnancy, and wonders was she just used as an incubator.
The third theme is "designer babies" and the ghastly mutations that result in this experimental program, funded by the DOD, the Department Of Defense.
And this leads Scully to believe the program is experimenting with alien DNA on children, who are pretty well monsters they are so deformed.
Staying in touch! I look forward to next week's Episode Three on Fox.
How the stars got cast in their roles - with Jimmy Kimmel: