When you reply all, it goes out to everyone on the To line and the CC line. Reply only goes to the sender. When we send out a mail to many people, you might see a sentence that says 'little 'r' me'. This means to use the small R instead of the Big R. That basically means to reply only to me instead of replying to everyone on the mail thread.
A mail is also referred to as a thread. That is because in the office, a mail can go on back and forth among many people so it becomes a chain of mail that started from one email. I'll use these terminologies in the next several example sentences.