"Atlas, At Last" in Borderlands 3 is a main story mission that can't technically be missed. Its chapter 9 of the main story. The plot points in the mission follow going through
*** Spoiler - click to reveal ***the Meridian Metroplex, discovering the Atlas HQ, defending it from Maliwan, defeating Katagawa Jr., getting a Vault Key, and moustaches.
Its recommended to be at around level 17 for this section of the game.
Check out this IGN guide over this section. Its very helpful and informative.
https://au.ign.com/wikis/borderlands-3/Atlas,_At_Last
The hyperlink for the page does have a comma in it however, that is actually part of the URL.