Question About Story Mode

So I'm on the last mission of "Purge". It gives me a 0/16 Questline, and it increases everytime I make a warp jump.

I assume that once I warp 16 times my game resets.

So my question is, if I start a new save file, can I NOT follow the story line, and just explore unlimitedly? I worked so hard for everything, I don't wanna see it all vanish in 16 jumps...