According to studies done before Plan B, the first of the morning after pills, was approved by the FDA, Plan B did not keep fertilized eggs from attaching to cultured layers of uterine cells, and more recent scientific studies have disproved the “works by preventing implantation” theory definitively.
What the drug actually does, conclusively, is delay ovulation. See, to put it bluntly, it takes a few days for sperm to swim up the Fallopian tubes, find an ovulated egg, get into position, and then fertilize it. Morning after pills typically delay ovulation for a few days, until any sperm will have exceeded their use-by date, with a big dose of a hormone, while some also thicken uterine mucous to make it harder for sperm to swim around. (…)
But the drug only works if you haven’t ovulated yet. Women who have already ovulated before taking the morning after pill still get pregnant because there’s already an egg in their Fallopian tubes for sperm to get to, and it can still implant in the lining of her uterus.