My main mission marker is gone

I never finished that second Zero mission, it was the only marker left on map, but my PS2 would have gone out of the window if I had tried it again...

^ yes it can be for sure, I'm well used to playing games like rhis but this one chucks a few curveballs in. Went to go to a main mission marker last night, snuck there no problems, In the same area was a bow side mission so I did that, no problem.
However when that mission finished because of the orcs being alerted, three captains and a load of heavies all ran to the area and after briefly looking around and not finding me they formed a patrol pattern right over the main mission marker! So I really
didn't want to get involved with them as I had no Intel on any of them. I had to go and find another mission which was miles away. Things like this I find annoying.

if a mission does not have a marker you need to advance the story with other missions!

On the mission select screen is there a marker next to the mission showing if you got one? And aren't they every 5th mission or something?

Click on any empty part of the map. You'll get a box that will pop up with the options 'Move Marker' and 'Remove Marker.' Select Remove Marker, and it will be gone.