A possible plot could be that the baby is in danger due to Irene's past enemies. Sherlock has to use all his skills to keep Irene and the unborn child safe. Along the way, they both realize how much they care for each other and the future family they could have together.
Perhaps Sherlock discovers Irene is pregnant through his brilliant deductive skills. He then decides to take on the role of protector, which is a big change for him as he's usually so detached. This could lead to a whole new dynamic in their relationship, with Sherlock learning about emotions he never knew he had.
One idea could be that Irene tries to keep her pregnancy a secret from Sherlock at first because she's not sure how he'll react. But then as her pregnancy progresses, she has to rely on him more and more, leading to a new level of closeness between them.