E-mails are a way that Michael Thorton keeps in touch with those he meets, allies and acquaintances alike. Enemies also email Thorton, either to threaten him or to arrange meetings.
The Alpha Protocol agent also uses his secure email account to as a dropbox to send information to himself while in the field. He also uses his email to send information, either to the brave journalist, Scarlet Lake to publish, to The Clearinghouse as information for purchase, or to Halbech as blackmail. Either through this, or through other people, he can then access funds sent to him to fund his operations. Thorton also receives his intel from The Clearinghouse through emails.
Replying to emails works the same way as the Dialogue System, players are presented with options that will determine the email they send. Unlike dialogue, selected emails will be shown to the player before actually being sent to the other person.