This isn't an omegaverse and Sherlock and John aren't an Omega and Alpha. But Sherlock gets pregnant anyway. I don't care if it's a unique case or it has already happened before to somebody else.

Possible scenario: Sherlock has been kidnapped, held captive in some secret facility and experimented on, but doesn't remember much (drugs). The experiment had studied male pregnancy, but Sherlock didn't know about it until much later he got pregnant with John's baby.

The pregnancy is complicated, Sherlock needs a lot of care and medical attention. He's also not sure he wants the baby and possibly has a breakdown and attempts abortion.

Good ending or not is up to you.