In order to get access to Atlantis, you need to complete a mission called The Heir of Memories. This is a series of missions that was added in the free update for Assassin's Creed: Odyssey. You need to complete these missions if you're planning to visit Atlantis.
To begin The Heir of Memories, you first need to complete the storyline involving Pythagoras.
However, there is a faster way of visiting Atlantis. All you have to do is to choose the option "The Fate of Atlantis" when beginning the game. You receive a choice, shown in the screenshot above. If you choose "shortcut", a new save will be created, with a level 52 character. This won't delete your old save, provided you've saved manually.
Remember that the DLC contains spoilers regarding the events from the base game.