To unlock the ??? Cave, you first have to kill Cloud of Darkness which you already did if you follow this walkthrough. Now reload the game with the save after end credit (save slot with the 3 stars), this will bring you back to the Crystal Tower. 

Talk to MogNet on The Invincible as Luneth, you should receive a new mail from the 4 Old Man, read it. Next, change the top character to Arc and talk to the MogNet again, this should prompt you a new mail "Saronian Legend" from king Alus which tell you about a legend of a falling star into the sea. 

That's it, now the ??? cave is located at the south sea between Floating Continent and Doga's continent, see map below:

The ??? Cave has only 3 monsters:

• Yellow Dragon
• Green Dragon
• Red Dragon

They all drop Elixir and Onion equipment. The cave is pretty short, only a few steps toward Iron Giant.