Mary believes that she is having a cryptic pregnancy, but her doctor and her boyfriend don’t believe her. After she gives birth at home her child is taken from her by mysterious government organization, Mary has to fight her own self doubt to recover her child and prove her sanity.

Kind of like a horror retelling of the Jesus birth story... in concept, it sounds good, but in its current form the logline isn't working.

It's too wordy and most readers won't get past the logic flaws.? Also, best to define one goal, and in this case, her sanity pales in comparison to finding her baby.

When her newborn is taken by a mysterious government agency... (then tell us what the mother must actively do)

As the others have said.

If I think I understand what the unnatural "horror" aspect of the story is, it would seem to me that she would become pregnant in spite of being a 100% celibate, authentic virgin.? No man has gotten so far as to 1st base with her.? So of course, she would think it's cryptic.

And then she delivers.

And then the child is kidnapped.