In the first few hours
Every time a sick person coughs, she expels some 2,000 virus-laden droplets. If you inhaled any of those (or touched a door handle coated with them, and then rubbed your nose or eyes), they have floated through your nostrils and are burrowing into your airway's cells. Unlike colds, which attack the nose and throat, the flu virus can travel into the lungs.
Your immune system goes on the offensive immediately. It begins churning out antibody and T cell soldiers that latch on to and destroy the virus. Had you been vaccinated against this particular strain, you'd have antibodies stockpiled.
For the next day or two
You're unaware that the virus is now using your body's cellular machinery as a copy machine. Swollen with rapidly multiplying flu, the infected cells in your body begin bursting like water balloons, spewing virus everywhere.
You are now contagious. Hence, you should always sneeze into a tissue or cough into your inner elbow.
By day four
Your immune system can't keep up with the furious flu spread. Symptoms hit you like a freight train. You can go from feeling peppy at lunchtime to being bedridden by 5 p.m., beset with fever, chills, headache, and crazy-tender muscles. (Taking a few ibuprofen can help ease the aches.)
It's not the virus that makes you feel like crap. The misery stems from inflammation, the result of an immune system in "code red!" All of your body's energy is being used to slay the flu; you can hardly muster the energy to walk to the bathroom.
To keep dead cell debris from clogging up your lungs, you develop a dry cough. Your throat starts to ache from the irritation, which can trigger a release of mucus. A saline nasal flush might help.
For the next three to five days
The only things that can really help you now, antibodies and T cells, are locking on to their targets. You're stuck in bed. (If you started taking prescription Tamiflu right away, you might recover a bit faster; otherwise, don't bother with vitamin C or other OTC fix-its. Stick with tons of fluids and rest.)
If you're really unlucky, normally harmless throat bacteria have descended into your lungs to feed on dead cell remnants, putting you at risk for pneumonia.
After about a week
Assuming you've escaped pneumonia, your immune system finally stamps out the flu virus. Whew. Your inflammation slowly subsides, as do your symptoms. But you may still be contagious for a day or two more--and it may take another week to feel like your normal, healthy self.
Wash your hands. It's the single best way you can fend off a new flu virus. Scrub your mitts with soap under running water for at least 20 seconds after shaking hands with people or touching communal stuff like a bathroom stall.
Sources: David Greenberg, M.D., Sanofi Pasteur; Walter Orenstein, M.D., Emory University School of Medicine; Flor Munoz, M.D., Baylor College of Medicine; William Schaffner, M.D., Vanderbilt University School of Medicine