In 1.35 you can lose all the story part in the game. So backup your saves until this is fixed.
It has to do with mission waypoints impossible to reach anymore.

Here are the details:
http://steamcommunity.com/app/275850/discussions/2/1474222595296673526/

Thanks for the notification, I just used a portal for the first time so could easily be hit by this if I'm not careful.

Thanks for the heads up. I'll admit that, as of 1.3, I'm clueless about where I need to go and what I need to do any more. I'm running the Atlas path, as per usual, and also chasing Artemis and the other Travelers. So far (minor spoilers for anyone even more clueless than I am (unlikely ;-) ) I only have one glyph (the #2), no idea how to get any more, the Atlas count is up to 7/16, I have essentially no cash on hand, and I'm still a gazillion light years away from the center. Other than that, everything's fine. ;-)

Polo seems cheerful, so there's that ...

And about Portals:
If you use one and don't see one behind you when you pass it, then RELOAD THE LAST SAVE IMMEDIATELY. This is also a bug that will screw up many player's savegames, because: how would you ever suspect this to be a bug? All seems normal, but you can't progress the game without return portal and you will be stucked...:(