1. Inapplicable; I think you have a VN in mind. The plan is more analogous to Free Cities mechanically (though not slavery-focused).
I had all kind of games in mind, and what I say apply even with game mechanism like Free Cities. But I'll not starts talking about this, because there's a way bigger issue that you having no clue regarding what pregnancy imply for a girl.
And this issue is this:
2. Time passes in 1-week increments. Part of the design up-front.
Wait, you want a realistic fertility algorithm, thinking about a sinusoidal model for it, this for a game that have one week increment ? God... But what have you been taught in school ?
It shouldn't be the 51yo guy I am that have to do a Biology 101 course for you...
The menstrual cycle follow a lunar month, therefore it's strictly a 28 days cycle. Said otherwise, every 28 days the periods starts, and with them a new cycle starts.
Note: Of course, there's variations and some women never achieve to have a regular menstrual cycle, but for the vast majority, girls have a regular menstrual cycle. If not at first, it will become regular when they'll be 15-16 years old.
Ovulation happen between the 13 and 15 day after the starts of the cycle, and the ovum life expectancy is only 12 hours. Therefore, there's only 2 days every 28 days where a girl can possibly be impregnated, yet for only 12 hours during this period of time.
BUT this is without counting on spermatozoon. Inside the vagina, and the womb, its life expectancy is between 75 and 120 hours. Therefore between 3 and 5 days.
When you put everything together, every 28 days, there's only, at most 5 + 2 days (+ 12 hours if ovulation happen at the very last moment) where a girl can be pregnant. What is... well, one week, and therefore in your case one of your in-game time increment.
Side note: Despite this, for many reasons girls are right to consider a two weeks period as being at risk. Better safe than with an unwanted pregnancy.
Now, what it mean for your game ?
Well, it's simple, it mean that whatever the girl, as long as she isn't part of the exception that have a none regular menstrual cycle, there's only two patterns that can apply to her:
Either she have 2 safe in-game period, and 2 in-game period with a moderate risk of pregnancy, or she'll have 3 safe in-game period, and 1 in-game period with a high risk of pregnancy.
And this pattern being applied to 28 days cycles, it will stay exactly the same whatever month you'll look at.
There, you have what you are looking for. Randomly pick one of those two patterns, and you'll have exactly the same behavior than whatever realistic fertility algorithm you can come with.
Would your game be based on one day increment, it would obviously be something different. But your game is based on one week increment...
4. Nope, there won't be any story to worry about; not a VN.
You understand that when I talk about "story", it was in a global way ? The girls will not just fuck, right ? I mean, you don't want to put a realistic algorithm in top of a game where girls do nothing else than waiting for the player to fuck them, right ?
And it happen that pregnancy will affect what they are doing else than fucking. In fact, it will also affect them when they are fucking.