When you enter Fort Condor a man will be waiting at the entrance to ask you to assist in the battle. Agree to help him and head up the mountain. Talk to the man sitting at the table in the center of the largest room. Agree to assist him with the battle and then scale your way up to the top of the mountain. Talk to the man staring out the window.
The actual time your supposed to do this fight is the first time you pass by on your way to Junon. However, if you are like me, you skipped it. Maybe you didn’t have enough money to throw away at units for the fight, maybe you didn’t think your team could handle the final boss if you failed, maybe you just didn’t want Phoenix Materia that badly, maybe it was all three! Or maybe you just missed it all together. Either way, this place is a breeze now that you are leveled up, and you won’t have any trouble fighting the final boss.
Don’t get me wrong, the mini game is pretty fun. But it’s also pretty pointless, it’s a time sink, and it’s a big waste of precious gil. I suggest not playing, not even reading the instructions. Just start the mini game.
The boss you end up fighting for “failing” is a joke at this stage in the game.