Take a 12v
meter and test the input side of the controller for voltage. If there is no voltage then there is an issue with the panel, connections or wires. If there is voltage then test the output or battery side. If voltage is showing on the input but not output then the issue is with the controller. If there is voltage on both sides then test the connections where the output wires terminate. You should see almost the same voltage and to the battery connections. If not then check that fuse. If all looks well then the batteries are suspect.
Since you batteries got totally discharged then it may be a better idea to pull them out and put them on a separate battery charger to see if you can salvage them. Purchase a hydrometer to test each cell (if they are flooded cell batteries). If any of them are bad then its time to replace both batteries.
If you can post the solar panel size, controller make and model and battery make and model.