One Son (2) - S6-E12
Corrected entry: At The End of the season 1 finale, The Erlenmeyer Flask, CSM is seen placing the alien embryo (pickled in a jar) in a box somewhere deep in the Pentagon's storage facility - yet in season 6's One Son, the embryo is back in the flask, in the freezing solution where Scully found it in the first place. (00:30:35)
Correction: The Smoking Man, who put the embryo in the pentagon's vast storage room in season 1, has direct access to the pentagon at all times and is extremely high up in the ranks of the conspirators, it's more than plausible that he could have taken the embryo back from storage and returned it to the freezing containment if it was needed for further tissue/testing.
Purple_Girl