Your ship should be where you are, your crew flies it to your location for you. There is usually a exit to starship option when coming from your stronghold, if it was greyed out, you haven't acquired your starship yet, or something went weird.
Have you completed your class story on Coruscant, that gives you your ship (that mission step occurs with several mission, which is why I ask, the mission of getting your starship at the end of captial world class story is one of them)? And have you tried a Fleet pass (CM has them for relatively cheap if you've earned any Cartel Coins from achievements). Also have you tried queue-ing up for Warzones, or Flashpoints through Group Finder? Group Finder Flashpoints give you the option to either exit to your previous location when you leave, or to a set exit point, usually on Fleet. If you can get to Fleet, you may be able to access a hangar, or go back to Coruscant via that shuttle and see if you can then get on your ship.
Also, have you tried resetting that mission, to see if it unsticks you?
