Guild Wars 2

On the green marker I’ve a prompt to exit the Omphalos Chamber but not the one to enter the story instance.

I don’t think the entrance to the story instance is inside the Omohalos Chamber. Try exiting back to the Grove, and look around near the entrance for a prompt to continue the story.

That’s part of the problem, the marker is in the chamber not near the elevator as usual

That’s just marking the exit from the instance, as you need to leave to get to your story.

I tested this today with an alt, and the entrance is in the Grove, a little way north west of the entrance to the Omphalos chamber, about halfway towards the asura gate.

Found it, thank you