Sheltering in place during a pandemic flu means to remain indoors and/or avoid congregating in order to save lives or prevent exposure to a deadly disease. In the event of a pandemic flu, if you hear media reports telling you to shelter in place, some of the things you may be asked to do are:
Stay at home, especially if you are sick
Avoid crowds or large groups of people
Use the items in your emergency kit to avoid leaving your home
Turn on the battery operated radio in your emergency kit and tune it to a designated news channel
Listen for messages from public health authorities telling you what to do