Methotrexate, when it works, stops the rapid division of cells. I think it was originally developed to stop the rapid division of cancer cells, and they found it also had this effect on embryos since they also have rapid cellular division, making it a useful non-surgical method of treating ectopic pregnancy and saving the tube. If the metho works, the cells will die and become an inert mass, and then the idea is that the downward, pulsing motion of the cilia in the tubes would push it down into your uterus. You would not notice it coming out, it would come out as part of a period or just as a little dab of something in discharge (the embryo is very small at the point when metho would be used, maybe the size of the "o" in this sentence, I think).
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