Flu-like symptoms can also be a sign of an STD.
None of her symptoms would be a result of a surge of hormones from birth control, and beyond that, if she were having side effects, it is highly unlikely it would begin four days after taking the morning after pill...it would begin in the first couple days most likely.
Take her to the MD and get tested with her if you can get an appointment - there are also various STD clinics that offer reduced or free testing depending on your income if that is an issue - just look up your county health department and it should have any information you need.
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