To find Atlantis you need to complete the side quest "A Family's Legacy". This quest is unlocked automatically after the main mission "United Front" in Episode 7. You will not be able to do this achievement if you do not have this quest.
The following section contains minor spoilers.
*** Spoiler - click to reveal ***You will be asked to go to the island of Thera. You need to retrieve an ancient tablet which can be found by scanning the area with your eagle. Once that's done you need to follow rays of light to a giant stone door. This is a little riddle sequence where you have to smash some doors and move some objects in order to make the light reach the door. This will power it up so that you can enter. Behind the door you will find access to Atlantis. You will meet Pythagoras which will also trigger another endgame questline.
You earn this achievement right after you met Pythagoras.
If you prefer visual guides here's a video that will help you out:
Note: Video is not mine - all credit goes to PowerPyx.