So what happens when you log back into the game? Does it place you where you left off? Does it not let you continue? Going to need more information on the issue your experiencing.
go to your mission log and see if you click on the mission, there should be a play button that allows you to continue where you left off and move forward. Make sure your not in an instance like your ship, stronghold, etc to ensure it pops up.
If that doesn't work, worse case would be to reset the mission, again make sure your not in an instance like your stronghold or ship, just do it from the fleet.
