It means they won't be arguing their innocence to the ADRVP (the government-appointed group who assess show-cause notices and any responses to them in order to decide if the players are likely to have doped). Unless something strange occurs, it's pretty much a given that the ADRVP will conclude they have doped and will put an entry onto a 'register of findings'.
Once this occurs, I believe the infraction notices are sent and the players are referred to the AFL tribunal. The players can still argue their case here I think, and ASADA will argue theirs. Then, they are found guilty and punished.
If either side (ASADA or Essendon*) are not happy with the outcome, the next step is for the matter to be taken to the CAS - the sports court (in Switzerland I believe). That will drag the process out a looooong time.