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-also in your log select the quest you want - if its atlas it will guide you in the galaxy map or select the autophage one
There is no alternative.
This was after I scored a sentinel interceptor, and flew around in it for some time which triggered a secondary quest. The autophage had tried to "hack" the ship, they said because they only scanned for the 3 main lifeforms and thought my ship had no pilot.
All you have to do is get to the point you get that choice. If you choose not to reset, to refuse the Atlas, you have finished the Purge and qualify for the autophage quest to begin (assuming you have also visited a harmonic encampment and done the requirements at one of those).
Lots of very incorrect information is out there on what the requirements are for the autophage mission to trigger, including people saying you have to finish Trace of Metal and that you have to go to a different galaxy, etc. Neither of those things is true. You just have to complete "The Purge" and engage with a harmonic encampment. Refusing the atlas and not resetting the simulation is one of the options for completing The Purge.
To the OP, regarding the game telling you to return to the atlas. My guess is you already did visit and chose not to reset the simulation (i.e. you refused the Atlas). If that is the case, the game is misleading you when it says to return to the Atlas. You're done.
See the wiki[nomanssky.fandom.com] for additional details.
The Atlas Path quest will remain in the log and either it or the Space Anomaly quest will become the default quest whenever the log resets itself. Potentially the OPs quest is now defaulting to the Atlas Path?
Incidentally, Trace of Metal was originally a pre-requisite. It was removed. That info was not incorrect, but it is now out-dated.