The two medications are very different. Emergency contraception (also known as Plan B or the "Morning-After Pill") is high dose progesterone (a hormone which is also found in birth control pills). It helps to prevent pregnancy by delaying ovulation or preventing an egg from implanting in the uterus. If you take emergency contraception but become pregnant anyway, the medication does not harm the embryo, and if you choose to continue the pregnancy there is no higher risk of complications.
The abortion pill (also known as mifepristone, mifeprex, RU486, or medication abortion) is a progesterone blocker. It terminates a pregnancy that has already been implanted. The abortion pill has a 96-99% effectiveness rate. If the abortion fails, serious birth defects could result; for this reason, patients must be prepared to complete the abortion with an aspiration procedure.