From the top down, you should have:
The flush valve
The flush valve base
A rubber washer
The bottom of the cistern
And a large nut that holds the flush valve base in place.
If you haven't taken the cistern off, the nut will now be sitting in the space below the cistern.
You can't put it back together without taking the cistern off.
Mind you, if it's gunked up in plumbers' mait it's probably been bodged before. Maybe it is time for a new flush valve, they're not terribly expensive.