The de-nitrifying bacteria will still be there and likely thriving!
Do a BIG water change... (certainly more than 50%) and put the rock back in (It'll need to re-culture, and the die-off on it now should provide plenty of "food" in the meantime as it re-cultures.) Also turn all the pumps and such back on.
Let it run that way for a week or two, then do another bg water change and if parameters are good, I'd put fish back in it!
(Unless everything in the tank is covered with algae at this point... in that case, it might be easier to just take everything apart, clean it with vinegar and start over from scratch.)