POPFile is a proxy that does two things. First, it listens to any commands issued to it by your email client and passes them along to your email server. When your email client asks it to retrieve a message, POPFile adds an classification tag to the message as it passes it along to your email client. Secondly, it adds a link that will take you to the message in POPFile's history so that you may reclassify the message if POPFile made a mistake classifying it. Both the link and the tagging functions are turned on by default but are optional.
POPFile does not have the ability to retrieve or check messages on its own, it simply sits quietly passing along any commands it is issued by your email client to the email server.