Is my story over?
Since the ending is mentioned I will use spoilers too.
The main story quest in NMS is the one called "Artemis Path". The Atlas seed gathering task is actually another unrelated quest commonly called "Atlas Path". While the two are obviously related at lore level - both are about the Atlas- they are otherwise separate as far as gameplay is concerned.
The Artemis Path final steps - The Purge & New Beginning - do indeed end with the choice of either "resetting" the simulation and traveling to a new galaxy (notice that on a pure gameplay level the old galaxy is not deleted an for example still available from the portals at every space station) or just staying in the current one. Either way, that is the end of the main plot (notice: I think you are still able to return later to reset the simulation if you refuse the first time, but I don't know if this is still the case).
Coincidentally, this is one of the two standard ways to go to a different galaxy outside co-op / portal abuse - the other being reaching the Galaxy Core. While the core can be reached multiple times, the Atlas Path can be completed only once. That said it is worth noticing that the old community weekend missions available from the Anomaly had some sort of basic plot that somehow tried to follow up on the main one. Currently, that seems to be on hold in favor of the expedition feature. The old missions seemed to point to the nature of the "red glass" that haunted Artemis, but so far nothing else has been revealed. I suspect that the next story advancement will be made in a still-to-come expedition in a big future update that may introduce some sort of Atlas related enemy but those are only speculation.
So, what can you do now?
- explore the new Outpost feature and build a city with actual NPC.
- join the expedition mode when is available. Requires starting a new save and is more of a speedrun even with a set duration
- do other quests you may have missed like the Living Egg one, Abyss one etc
- complete the Atlas path if you don't have already.
- just do what you like... base building, getting the perfect companion egg etc...