Can a US citizen file for divorce in the US if he was married to an Egyptian in Egypt

Yes. Many people get married overseas. You get divorced where you reside.

Are both US citizens and are you both living here? Was the marriage on US sanctioned soil like an army base etc ?

The general rule is that if a marriage is legal in the jurisdiction in which it is entered into, anywhere in the world (except for locations that recognize multiple marriages), the marriage is treated as legal in the US. It doesn't matter if neither of the parties were US citizens at the time or what legalities were involved in entering into the marriage.

Dissolution of marriage in governed by the laws of each state, which can involve meeting specific residency requirements and so on. Personal jurisdiction over an individual is necessary to make property or support orders that effect that individual; however, personal jurisdiction over an individual is not necessary to simply dissolve a person's marital status or to make orders regarding custody of a person's children. A court has personal jurisdiction over anyone who is a petitioner in an action to dissolve a marriage. This operates under the principle that by filing the action the person has consented to the court's jurisdiction. Personal jurisdiction over an individual who is a defendant or respondent in a dissolution (called divorce in many jurisdictions) may or may not exist depending upon the degree of contacts that person has or has had with the jurisdiction.